I've attached a mod for testing the issue below. Instructions to reproduce the issue here:
1. Pick wanderer start (start doesn't actually matter, just need to spawn at The Hub)
2. The Hub has been replaced by only a number of unique squads as residents, numbered and standing inside their buildings. Feel free to verify they are spawned correctly so far by walking in their buildings and checking.
3. Talk to the wandering P4 Unit wandering around the town. And use his dialog to trigger the override.
4. Run away from the town until it unloads to allow it to flip the town, then return.
5. When you return many, if not all, of the uniques will be missing. Their squads spawned, but they themselves did not. And the P4 Unit patrolling the town will be missing.
I'm unsure why this seems to happen. Best guess is something about it seeing the characters as already in use, and so not spawning them with the squads. But I don't understand why only Bar Squads and Traders are being affected by it.
Anyway, if you need any more information, I'm happy to provide anything needed.