I've recently helped Sarwa or what's-her-name regain control of the Sarranids in my current playthrough. Everything went perfectly but then I realised several NPCs were missing from the world... apparently they're still part of the rebel faction, which shouldn't exist anymore, and I can't get to them (failed a mission because of that).
I imagine things like NPCs' allegiance, fiefs, rep, etc. are stored within the save file so... is there a way to edit those values manually, and is it safe to do so?

Don't know about that. I know that you can hack items, troops, parties, party templates and factions through Morgh's M&B WB/WFAS Editor, but that changes the whole module, not just the current "in-that-exact-save" settings and probably would bug the game even more. Sorry. :(
If someone would find that out, I'd also definitely be grateful for that.

PS: It's just "Arwa". ;)

Sometimes it can take a while for eliminated faction-allied NPCs to actually leave the gameworld (until they do they're stuck in limbo, you can't get to them and they're removed from the overworld). I believe it's taken around two weeks in-game time (if not just a bit longer) for one of them to leave my game. Just to be on the safe side you might want to make sure that every castle and town has been taken from that faction and that that NPC is not still riding around recruiting soldiers where you can't see them and that they haven't joined another faction.

(This is all assuming you're talking about Warband)