I'm not sure whats conflicting but I have been getting this random pop up about naming a book but no one is writing a book in the active household... is there some "invisible sim"? Thats writing a book across my multiple saves? Or its a mod conflict?

StoryProgression can allow you to choose book titles for inactive sims. The setting is here:

NRaas > SP > General Options > Options: Skills > Prompt to Title Written Books

You'd need the SP Skill add-on to see it, and it's off by default, but perhaps you enabled it at some point.

I don't know of another mod that allows this, but if you have any that involve skills, it's worth removing them temporarily to see whether the issue goes away. You don't need to save your progress; just let the game clock run for a while.

I've always kept the SP option off, but I get these pop-ups anyways, almost every sim day. I always assumed it came from a "writing is more fun and more autonomous" mod I use but I've never really looked into it so I'm not sure.

You'll know if it's SP-related because the SP pop-up will tell you the name of the sim writing the book, and maybe the genre. The pop-up I get doesn't give any extra info, it looks just like the regular prompt from my active household, except it's for random inactives who are writing a book at the time.

Doesn't seem to cause a problem, as these inactive sims are writing books with titles I choose. I do kinda wonder where it's coming from, though.

I don't know how it happens exactly, but it reminds me of how you can sometimes get a "three's a crowd" popup about a group none of your active sims are in. Just seems to escape containment and ends up prompted to the player.

If you don't mind missing out on books written by the town, a guaranteed option to prevent this is SP's Use Refine Writing Only. Skill Module required, under Options: Skills. This means inactive writers will only be pushed to practice their writing skill instead of starting novels.