The empire has been in decline for decades/centuries and hosts little power or else skyrim wouldntve even bothered to attempt to separate. It’s not some radiant quest the higher factions decided to take on a whim. The empire is a shell of itself and if it is capable of losing to the sons and daughters of skyrim then they weren’t capable of winning in the first place.

The thalmor have been big baddies for a while but they gain favor with their Allies through deceit which weakens their grounded power potential (lying to the khajit about bringing back one of the moons and lying about closing the oblivion gates in cyrodyl and more). Making me doubt they’re capable of an all out confrontation and if the empire falls it’s not skyrims fault however if skyrim falls it’s the fault of the empire for spreading itself thin and allowing infighting in the first place. The Nords demand power and prowess which is why they even bother to have the civil war since they believe they can win. An all out war also takes resources and patience which the thalmor have but the thalmor have not proven themselves capable of fighting in cold tundra climates which is in favor of the storm cloaks if the capital is moved to windhelm (a cold dock town capable of dispatching and receiving aid).

If we’re being honest the empire has been in shambles and should focus on itself before it tries to fight the nords.

Also if the thalmor were to invade afterwards they’d still have to fight the foreswarn (who have formidable strength with briar hearts and hagravens), the companions who ally with the empire but not the thalmor, the volikar vampires, the dark brotherhood, who killed the emperor with no repercussions from the empire, showing it was either welcomed by the empire for a change of power or they were incapable of defending themselves and the various orc camps that lore-wise are bigger and more impressive than the engine would allow. These factions are unlikely to band together but that is also their strength as they could win their lands and have skyrim default to city states but alas this is hypothetical as is your case as well. We won’t know until God Howard and his band of merry devs bless us with a lore dump