I got an answer to this question from the aftertimes developer. Here I post the answer for everyone who is interested to know:
Answer:
This is possible! Just upload the new fomap, restart the server, get admin access, go to this map and use the "~regenmap" command. If after regeneration npcs will not respond to any interaction then kill them all and regen this map again:
1. Get admin look to see all crits on the map with "~run cheats adminlook 0 0 0" (and move your character by one hex to refresh fov.)
2. Kill all NPC on map with "`killmobs"
3. Then use "~regenmap"