Possibly contains irrelevant info, but just in case, brain dump ahead.
Same experience. I found that I couldn't enter Outpost Zimonja (used a city plan from the contest pack) at all while Sim Settlements was active (Also noted that attempting to use remote detonation did not open the dialogue while near it) and none of the recovery methods worked. I even used the nuclear options to kill the scrap the settlement via console and remove the workshop's ownership record with Rimfalltools. If SS was active, CTD on approach was guaranteed.
I also found that I had to refresh city plans due to severe lag and, in the case of Murkwater, a remote detonation was required. (Unlike Zimonja, it worked there) and start over. I had to do the same at Jamaica Plain as the plan was stalled with most of the plots refusing to refresh.
Also, rolling back SS still left the Zimonja severely bugged and only partially loaded. I tried to refresh the plan with no luck and eventually local detonation with full charges followed by the gavel scrap cleared the rest out.
Odd note - Maybe it was WHEN I did it, but I ran R2K's tool when I got into the settlement and it said no problems. I ran it again while completely nonexistent villagers were scrapping the rest and it returned 3 bad grids with 5 bad nodes. I killed them with the tool.
I also noticed the save bloat has been pretty nuts. It did drop 4mb after I finished the detonation and cpg 1 script, but rose back after the villager scrap was complete.