In RL Greenland's first colony fail was blamed first on the Inuit (who honestly told the folks who bothered to check on the colony after a huge long period of time had passed... the final nail was attacks from unknown people in ships who killed and stole people and the few survivors of the last attack had joined the Inuit.) Wouldn't it be funny for Sathar to be all "weszs didn'szz killzzsh themsss, wezsh ssssavessz fewshz leftsszs sss'beshindzzs"... and of course no one would believe that but what if they did find a few survivors while exploring themselves and did not go all kill happy/mad scientist because they felt the attacking party was a threat to the Sathar too and at that point in time they had no issue with the Core 4 yet. So you could conceivably have a few representatives of one or more races that are descendants of the survivors and part of the Sathar culture.

Actually the theories tell us a lot about academia's biases more then they have about the first colonies disappearance over the years:

Okay first bias was the heathen barbarian primitives did it! Okay totally politically correct bias for that time period but wrong.

Modern Greenland failed because theories include:

Died of plague: though some illness did hit, it turned out not to be that. Not so much a bias but a guess based on disease hitting Iceland and the Mainland's plague issues.

Failure to adapt: (not learning to build homes differently, wearing clothes that get you killed in that climate, not eating non-mainland farm type foods) which equaled starving & freezing to death... also disproven. The evidence does indicate they adapted just fine, took up seal hunting like the Inuit even when their livestock did not do well. So not the racist, stupid, stubborn, bigots imagined by the biased researchers.

"Climate Change": was suggested as that is the current Boogie Man but it was not that either yes it got colder but they adapted and did okay. 

The Church & Crown: got blamed those greedy Bishops & Kings stealing the peasants best land, crops and cattle... but though a few times in the first colonies history someone showed up for tithes & taxes again it looks like that was not a huge pressure on them. So that was probably not it either, even if the anti-church, anti-government & anti-capitalist types wanted that (the other popular scapegoat reasons in academia).

No merchants: It is now suggested the main income for trade was no longer being sought by the mainland, so this made it impossible to get lumber and metal (not a lot of trees & metal on that island so you need to import that) tools... merchant trade ships stop coming either because it was low profit to high risk margin to get to them or because plague in Europe made for less merchants. Now that could be a big problem for any colony if you can not maintain your buildings, ships or other needed technology you need to survive in the way you want to you have a huge reason to leave if a ship does cruise by. It also means no new people are coming to settle, marry or work to help increase the population or maintain it. That would be a big problem for a high tech colony too.

No catastrophe: The evidence is currently more for a mostly orderly leaving of Greenland by folks (most likely to Iceland), absent from most digs is anything of worth (indicating someone took it with them) and the skeletons indicate that the last where old folks, absent are any young people in particular no women in the late period. No women = no babies = no colony. 

Pirates: There is evidence of some attacks on the few farms at the end so it is really looking like the Inuit told the truth. Mostly people just left, and then pirates showed up killed a few folks, took the rest as slaves and a few (I think it was like less than 5 people like one women and a boy or two) escaped and became Inuit tribal members & by the time the crown said "Hey don't we have a colony out in the ocean some place? Maybe we should check on them?" those folks were either dead of natural causes or had moved with their Inuit families to where ever.

One guy is known to have died of old age in his sleep as the Icelanders went to check on Greenland long before the mainland and they found absolutely no one at any of the known farms, except one dead old man in his bed, whom they buried. I think they couldn't even find any Inuit at those folks camp areas. My gut is the Icelanders decided to check on Greenland one last time to make sure no one wanted leave that was still left behind as they where also noting less ships from Mainland. 

The archeologist can even date when farmhouses where closed up based on when the the insects that live around human farms & homes died off. No joke.

So a colony as a Archeological Site should have lot's of mystery and possible causes for abandonment... so there should be lots of clues some conflicting that play on player's biases just like many of the above theories clearly bring out RL researchers biases.

Besides your suggestions and (Yazirians should really have several missing colonies I think) I would add: Sathar, primitives, blue plague, corporate wars, lost ship, racial isolationists, secret labs/research stations, illegal mining (with or without slave labor), off the map prison camps (facilities where beings where experimented on, tortured, possible genocide even), ancient technology activated that did something to the colony, Arsenal of Freedom ST scenario (there was a planet/colony that used to make top notch weapons, but no one knows why it stopped trade after a certain war or conflict... reason an adaptive weapons system that wiped out the colony when they tested it) and don't forget gender based power structures as a colony hook, males in charge, female in charge, no men, no women hooks and so on. How about a UPF planet has had a rash of kidnappings and it is beginning to look like the children are being taken off world... a colony that has a sterility issue might first have kidnapped adults but maybe if that failed went for young children instead to replace their numbers (Star Law is trying to figure out where the kids are, clues lead to an "abandoned colony" that is not abandoned). I think there should be several religious colonies for sure, hidden but viable. 

I also have an idea for Yazirian Hippies... they are heretics by everyone's standards, peace, love and brotherhood for all sentient beings, and they believe all sentient life is connected and that the Universe is the Garden not just one planet. So they do not necessarily agree with destroying parts of "the Garden" in favor of other parts AKA not fans of terraforming, they see all life as part of the garden and all intelligent life part of the Family, all planets are part of the Garden (therefore all of natural life is worthy of protecting and all must learn to live in harmony with the Garden). So anti-traditional warrior culture (some are true pacifists like the Amish, others teach peace but it is okay to defend yourself... think warrior monk) & anti a lot of the Fo1 activities & teachings. They believe the Fo1 has suppressed the true teachings of the Prophets or Enlightened Ones of Yaziria as revealed by the great teacher who herd the voice of the Garden warning of the doom towards their homeworld. So more than a few of these colonies should exist failed & successful. Space Hippies...

I like the idea of a mysterious colony remains that is not human, dralasite, vrusk or yazirian... yeah someone had set up homes, farms, all the things a modern culture would want at a minimal colony level but it had been abandoned some time ago but not that long ago... why, who are they, and what where they doing?

I am also thinking of Sathar Archeology ideas... I really should work on my Sathar Pompeii/Ground Zero, battle grounds and so on ideas. In my head the Sathar are still pissed & paranoid about being destroyed ruthlessly in the past by someone or something.  

Lost cities... don't forget tales that make people want to find the Sci-fi El Dorado, the Holy Grail type stories, healing, life ever lasting, technology that could change the universe... the actual thing/place usually does not live up to the tale. Power, wealth and living for ever are common themes...

There is a bad Kung Fu movie in which everyone is getting killed over an ancient discovery and the hapless couple ends up being used to smuggle (with out them knowing) the discovery to a man who wants to rule the world with it... lots of chasing, people getting killed, chases, hostage situations and all sorts of mayhem involving the thugs & authority figures (like the law) and it turns out to be gun powder (a now common well known explosive). The basic scenario is sound though... for a plot line only the discovery need change.

 

There is also the trans-dimensional planet idea in sci-fi, in that every x number of years a planet appears (with a colony on it) for a set period of time and then disappears again to the other dimension. Thus the planet is mythic but still very real. Stabalizing the planet so it no longer pops in and out are often themes, sometimes the populace can only breed in one universe/dimensional state or there are other side effects or dangers to appearing/disappearing planets.

I like the Vhim angle for the lab.

On the lost colony thing maybe the humans and vrusk decide to back track a bit looking for missing colony ships, drals could finally get some data recovered and figure out they might have a missing colony or two too... I have always been of the opinion Clarion had prior to humans a Dralasite Colony on it, I was leaning toward humans killed them but the colony could have failed for some other hidden reason on Clarion that someone reactivated by accident (after finding the colonies remains) and now the current UPF population is in great danger from this lurking ancient terror that wiped out the first colony no one knew about.

In fact since the CoH is stationed at Madderly's Star which is also an exporter of mercenaries the revolters might have summoned help from there and a mercenary company with a priveteer may be in system now and the PCs could face some KHs action. 

For this you could use the trappings of Nazisism. Including concentration camps for sapient aliens like none human members of the core four and for the dirty alien lovers from among humanity.

Lost civilization buried under the sand, mysterious cults in a more mysterious culture, an evil demi-lord hovering over everything (and coinciding cult as well), and an underground city to nurture everything.

There really isn't much to be rewritten...throw in some more modern tech and have a sathar borg-creature as the demi-lord. Park it in a desert region of an uncivilized world near the edge of the Frontier.

I gotta give that to shadow shack for the win. I also seem to remember that shadow also rework the Keep on the Borderlands as a sci Fi adventure if I'm not mistaken.

Yes, albeit just the keep itself. It was initially a pirate base to supplement Outpost One & Slave City One for the Star Devils on Volturnus but I never actually used it. I still have the maps floating around somewhere, same layout but with plasti-steel structure and heavy lasers/recoilless rifles/machine guns replacing the ballistae & catapults. I ended up swapping it for a "Sea Port One" at the southern end of the Volturnus map as their main HQ.