Edit: Confirmed to be related to Wide Gate geting destroyed, make the ground under it permanently “unpathable”, and some how effect all the buildings, gates, and fences in the settlement.
Removeing the gate manually also create the same bug. Luckily I have a safe file right before the bug happen.
Thanks for reporting this. A fix is coming in v1.0.1. You will have to delete the wide gate build site and the wall segment on each side of it to fix it though.
However, the bug where destroying a wide gate made the space unpathable is fixed, so you shouldn’t get into this situation again.