I recently published a mission that contains a map where the player's BOFFs and NPC mobs disappear and respawn in odd places. I'm not sure what the cause of this would be and I don't really have a way of troubleshooting this. The mission ID is ST-HPGUY3BMQ. The map is called "Detention Center," which was made using the Empty Ground Map.

"No matter where you go...there you are."
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First step: duplicate map, see if the problem persists. If it does, then try copying the map manually. Turn snap to grid off, highlight everything, copy, then paste it onto a new empty ground map (if it doesn't let you, unselect spawn points and individual members of ground mobs.) You might also try moving the assets to a different part of the empty ground map (raise it up, try to avoid hanging it off the textured basemap.) If the problem persists, then it's likely a problem with an asset or how you put that map together.
I've used the empty ground map a lot for similar kinds of builds and haven't encountered a problem like this. What I'll note for differences: the holding cells (I've never used those assets), the recessed ceiling lights near those holding cells (seems like NPC's kept spawning near those, if not directly under) and the small rocks on the floor (I've used them a few times but not fully across a hallway like that. If these are the problem, and you placed them across multiple sections, you might have built something that the pathing system can't handle.)
If all that fails, then look for anything that you did with that map that another author might not do. This includes the creative use of assets and random artifacts of your building process. Clean up anything that might be lying around (I noticed a random block on the mini-map) since that will at least simplify the list of things you have to consider.
If everything fails, I'd just make it a shorter map and take out combat. Players probably won't notice what happens to their boffs here if they're not needed. Knock out guard, rescue people, proceed to lab (and maybe have a little non-combat exploration with optional dialog), done. If this problem ever comes up again, then we can look for points of commonality.
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*edit* I know it sounds like a stupid question, but the editor creates pathing during the publishing process. It could be that republishing will correct your problem, provided that the problem was created during the original publish. It wouldn't be the first time that such things have happened.