Star Trek: Starfleet Academy S1-E09 "300th Night" ***Spoilers Within***

What about the physics of the Omega molecule would prevent them from synthesising it again, given that both the Federation and at least two other species were capable of doing so hundreds of years ago?

They weren't even that far off from stabilising it. In the Voyager episode, Seven managed to stabilise it for a few seconds. The original Omega Directive was put in place because of an accident, not because Starfleet's initial attempts to stabilise it (again, hundreds and hundreds of years ago) were entirely unsuccessful.

Since then, as others pointed out above, they've had 'The Burn' which wiped out warp travel anyway. Even if we can't imagine any other possible reason in 800 years, that seems like a reasonable one for abandoning or re-thinking the original Omega Directive.

I mean look it, I didn't love this little plot device either. Never a big fan of these galaxy-wide threats they're so keen on in modern Trek. But this level of nit-picking is just silly – we've had far worse than "Omega-47" in the last 60 years of Star Trek.

Sure most people love the one where they sling-shot around the sun to travel back in time to find some whales to save the day. What in the ever loving Trek was that about.

Or the torpedo that regenerates not only entire planets, but also well loved characters.

Or the space rainbow that grants you your every wish but just isn't enough for our hero, Picard, and lets you pick up old cast members and hop back out at any time you want but somehow not meet yourself and why did he go there anyway and not a little earlier and.. I just. What the **** was that anyway.

Or… etc. etc. etc. etc.

https://memory-alpha.fandom.com/wiki/Omega_molecule

A single Omega molecule was synthesized in the late 23rd century by the Starfleet physicist Ketteract on board a classified research station in the Lantaru sector. The molecule remained stable for a fraction of a second before it exploded.

By the late 24th century, Starfleet had come to the conclusion that Omega molecules represented a threat not only to the Federation, but to the entire galaxy. A chain reaction involving a handful of molecules could devastate subspace throughout an entire quadrant. If that were to happen, subspace capabilities like Warp drive and subspace communications would be rendered impossible.

(in the 800 years since that happened, Warp drive and subspace communications were already rendered impossible).

Another civilization in the Delta Quadrant was actually successful in synthesizing some two hundred million Omega molecules in 2374. They were able to keep the molecules stable.

By 3195, Starfleet had developed Omega-47, a synthetic variant of the Omega molecule with a destructive capacity in the same apocalyptic range as the regular Omega molecule.

800+ years and one "burn" later. And it's not even the same thing necessarily, it's a variant.

:shrug:

Except that it did change though. Evidently.

You don’t like that it did, fair enough. But it’s not a canon busting plot hole. It’s just something that happened in the near millennium of history we haven’t seen on screen.

Yes, sorry, yous are right. But the outcome was vastly similar. Or at the least was enough of a cataclysmic event which might lead you to imagine that some decisions around the safety of particular research projects might be re-evaluated.

And anyway, again, it's been so long. I'm just speculating a possible reason why things might have changed. There could be countless others.

Yes, policies could indeed change over centuries.

And, apparently, they have.

Core piece of lore? It was one episode.

And I thought your issue was that “one person manages to steal this previously destroyed never to be heard of again top secret molecule and that one person weaponises it against the entire Federation” – because not even the Borg could do that!

You only seemed to care about this core price of important canon lore after it was pointed out that none of what you originally said actually happened the way you said it.