Update:
So I tried disabling DEP for Stonehearth.exe, it isn’t letting me do so. By cancelling construction before any floor tiles were placed, I was able to tediously pound out this little gem. Unfortunately, my save corrupted:
So pretty… too bad 
Notes:
The problem IS linked to the removal of the final block of a building (or of the last tile of floor, at least)
Hope this helps.
With regards to corrupted saves, are they of any use to you, Team Radiant? Is there anywhere we can upload them?
Edit: Also, can anybody else confirm this bug?