It looks like you have used my plan. I'm not ignoring you, it's only been a couple of days since you posted and I only generally check Nexus posts weekly, and at present I'm away from home so can't even log in to the site.
The plan has been tested and many others have used it successfully. Therefore, I suspect it may be an issue with the scripts (amount and lag) that may be running in your save.
Apparently, plots will detonate when they upgrade if you have Demolition FX setting set to ON (second to last setting under gameplay). The left over pieces can remain until a script runs to remove them.
Double plots have previously been reported where a city plan upgrades - a new plot is added and the old is removed, script lag can cause the old plot to be delayed, or even left is the script is dropped due to the number running.
I haven't seen this happen as I only upgrade a build plan's level and don't change the plan or move the plot.
More issues can occur if you have settings which allow for remote upgrading of city plans (that is having the city plan upgrade when you do not have the settlement cells loaded in game). I recall Kinggath mentioning something in one of the previous let's play that the game doesn't like removing objects when you are not in the settlement???.
Abernathy also has the 3 vanilla settlers, which depending on what settings are used, sometimes can assign themselves to plots and change the plan.
You could check your save with Fallrim tools for possible script issues, (someone else or reading the documentation would be required as I am not that knowledgeable in its use).
Alternatively you could try standing in the settlement stare at the ground and leave the game to run by itself for an hour to let scripts catch up. This might fix errors, but the save may have 'lost/dropped' some scripts.
You should be able to clear the settlement, I would first head to the city planners desk and remove the plan,(It's in the options somewhere but as I'm not at home I'm not sure exactly where). Next go the the settlement red workbench, choose manage (space) from the menu, and select scrap settlement. This should remove everything, however as it uses scripts to do so it might suffer issues if your save is already struggling with them.
Thank you for the response. I made this post when I was at the peak of frustration. A poor decision. I've spent the last 3 days trying to get this to work. I have seen most of what is in your post from other locations, only having found the explosion disable a few hours ago.
To clarify, none of this was meant as a smear and I have a few theories of what is actually happening, and a good part of it is being new to the mod and having seemingly broken things to a point that using that site is likely a bad idea to begin with. I cleared the site a couple times trying to reset it to fix the problems I was having, but it never fully removed everything each time I did this, the build limit bar was remaining more and more filled even after fully scrapping the place. I've got abernathy farm 100% scrapped atm, and it's saying it's hit it's build limit even at 200%. The 3 dunderheads there just stand around doing nothing, even in this state, even if I put something down.
One thing I found and have never been able to reproduce, was a save that crashed, where in which I went to the farm and a bunch of objects were floating in the air on what should have been a fully scrapped farm. I don't know much about this game's inner workings, but it smells like some construction script is stuck in there or the items are just largely intangible and invisible and for whatever reason they revealed there. I don't know. I'd love some insight on what might be happening, even if not a fix.
I do know that after scrapping your plan, Gav, it never fully scrapped no matter what I did. I absolutely LOVE your design aesthetically. It was gorgeous seeing over the commonwealth from the top of that tower. However it also has issues due to being in the triangle. I tried using the workshop framework (on a save branch that didnt get continued) to reset the area as a last resort and it nuked half of sanctuary and red rocket as well, which are simple basic settlements, but it was still a problem.
As my last standing theory that MIGHT work, is that I only just disabled the limitation of build limits for SS or Workshop... I forget which. It's ahrd to keep it straight with 3-4 different menus of options that all seem to maybe sometimes sort of cooperate and other times dont ((SS2 Terminal, SS2 Holotape, SS2 MCM, Workshop MCM, Workshop management interface)). It's horrendously convoluted to troubleshoot. It's possible after the first scrapping of the site, which worked well enough other than the explosions leading to CTD, they hit build limit due to the site not scrapping cleanly, and then started just standing around unable to build outside of it. That said, if it's not actually properly scrapping the place, which I have no real knowledge to verify, then trying to build there is a dangerous proposition even more so than it normally would be.
You know what? As an apology for coming off hostile I am going to make a hard save real quick and test this theory. Should be simple enough. Just.. try it again with the build limit disabled. See what happens. Worst case it crashes and I just walk away from the spot. That said, if anyone has any insight or fixes for any of the above problems, I'd love to hear it. Even if not a fix, knowing WHY it's broken would at least let me walk away having learned something.
due to the script lag settlers were slow to ever arrive so I just threw up a tower and a couple super basic plots and just.. "Launch" people to other settlements.