I tried cleaning the save file to see if that would help.
Eeek! You didn't use the auto-clean feature in Fallrim, did you? By default that will kill ALL unattached script instances, which in some cases are legit fine and should not be removed. We should warn people about the auto-tools when we refer them to things like Fallrim.
Dunno how much futher you are, but best bet is to revert to a save from BEFORE you used the auto-cleaner. And don't use the auto-cleaner
. Generally, and I apply this to myself as well, Fallrim should be used to "look but don't touch" and refer any info found to those with more under-the-hood experience.
I have had settlers become invisible, walk around under the world, and, like virtual photons, wink in and out of existence. I've had the "find owner" fail to produce any noticeable results - but the FIRST thing you should check is: when you use the option, does "Building Lot and Occupants" appear as a message? In DATA under QUESTS under MISCELLANEOUS, is that selected as an active misc quest? If both of those are yes, does using that option on any other plot achieve the expected results?
If it's working generally, but not on one plot: try refreshing the plot, just in case. Don't go anywhere until the plot finishes completely; can take a minute, or three, or five.
I only caught settlers walking around underground because I had ASAM vision on to Find Homeless and saw a disembodied red glow ghosting through my settlement. I followed it until it hit an animation marker, and then the damn settler popped UP through the ground into the aura and started using the marker. gg Bethesda.
TL;DR the game sometimes has a..... *flexible* view of workshop NPCs' existence. Try other trackers to see if you can find them; in Conqueror, for example, you can track my Soldier Rank or Role. I have found settlers wandering Far and Away over the hills and several cells distant, just standing there in the dark. It happens. If you can find the missing person(s), and you can use the console, you have some options to bring them home. Otherwise, don't worry about the plot: the game still considers it staffed and functional (tho of course this doesn't help if they're a merchant....). Lastly, if nothing else works, try assigning someone else to the plot. This may cause the game to grab the now-unemployed settler and assigning them to something else, which might bring them back from the Great Beyond to move to their new job.
Edit: if there are only a handful of active scripts, and no Suspended scripts, you're good there.