So if they are all gone, does that mean the Tholians no longer have any fear of the Taurus Reach? If so, any remaining Shedai technology could be a threat since the Tholians have the ability to use it and wouldn't be worried about waking any Shedai who would then enslave them. Shedai tech in the hands of the Tholians could make the Typhon Pact very dangerous.
If that were the case, then the Tholians would most likely have already used that tech long before. It's not like joining the Pact has suddenly made
the Tholians hostile to the Federation; on the contrary, they brought that pre-existing hostility with them when they joined. So if they haven't used that tech before, there's no reason that would change now.
Unless now that new pair's of eyes are looking at the Shedai tech and thought, hey, we could use this against the Federation or hold it is reserve as a MAD deterrent against any possible future Federation aggression.