Grim, I read your other post. I would be curious to see if everything remains OK after you return to another settlement after an absence. In my game, it seemed that process happened multiple times.
@Chef (and anyone else who's listening), here's that update I promised. I apologize in advance for its length.
I think I left off with my walkthrough somewhere around Abernathy Farm. A rad-storm and subsequent Ghoul Horde spawn (from True Storms) forced me back to Sanctuary, but that did give me chance to check if the plots where stable and to see how my level 3 Sanctuary would handle an attack. The plots didn't respawn and despite some frame-rate issues (I'm running a GTX 970, 4MB @ 2560x1600 on an old i7 @ 3.2GHz and 24MB RAM) everything went smoothly (well, as smoothly as 25 - 30 fps will get you, anyway).
After that, I took a detour to pick up Strong (I felt bad for leaving him wandering around Trinity Tower) and after finding him under a pile of raider corpses, we backtracked to Starlight. This took a bit of time to get fully refreshed and I did have some issues with my settlers bugging out if I had them assigned to a non-plot work object. They would invariably assign themselves as a scavenger and wouldn't re-assign to their original, non-plot, work object (regardless of my auto-assignment settings). I had to use an old SS trick to get them assigned... build (or simply find) an agricultural plot, assign them to the plot, and THEN assign them to the non-plot work object. Weird I know, but it works.
With Starlight in order, I was off to Tenpines. That was a smaller settlement and had no issues. I didn't even have to refresh my Logistics station that, if you recall, were giving me problems when the interior Logistics stations would refresh incompletely.
Oberland Station was next and I took the opportunity to pass back by Starlight to see if the plot refresh stuck. It did. No issues there. Oberland Station is, of course, another smaller settlement and it went smoothly, though I still need to return to double-check my non-plot trading station which may have issues, though it looked like it was still staffed when I checked it in WM.
My last stop last night was Egret Tours Marina. This one was the most interest to me, given that I had issues with the city plan not spawning plots after it's initial level 0 build. I'd rolled back to 3.1.5 because of this. When I arrived the refresh went quickly and smoothly with it's 2 or 3 plots. I didn't feel like waiting around for another few settlers to arrive naturally, so I saved, quit and downloaded a "Settler Spawn Button" mod. After firing that up and mashing the button a few times, I ended up with two new settlers and after a 24 hr rest (which seems to be the new normal for plots to spawn here at least) one of the settlers had started to set up a farm and a house... so, yay.
So... to answer your question. Everything seems to be working fine on my end, no respawning of the plots, no empty plots, no frozen settlers, no issues really other than typical SS quirkiness.
I'm sorry that I couldn't reproduce your issue, but I hope that you find something out of this ridiculously long post that might help you.
Cheers