Can it be that you have the Workshop Lag fix installed and active? I suddenly have this issue too and did dive a little deeper into it.
Yes, i do have Build High installed and Clean and Simple - Settlement Startup (single files). This is not up for debate tho. I used them before and had just brilliant results, a lot less CTDs and no, my FPS doesn't tank but i rather have between 55 and 60 FPS with a 1060 6G, even if i have 150 Turrets running in one settlement (it's kinda fun to see them come alive when an attack happens, they are the 20mm CIWS from Weaponsmith Extended or the PTRS Standalone). Anyway back to the issue.
In the last three weeks i established a complete new load order with some different and additional mods. Now i got the stage that i said, yep, everything seems fine. Suddenly WS+ stops flying, right in the middle of the pretty fresh play-through. Here is a step by step of what and how it happens:
1. Got Sanctuary and RedRocket settlements.
2. Did the Tenpines Bluff quest and while at it went to get Starlight DriveIn (I use the Starlight is bright again from Greekrage, really nice in my opinion).
3. Got the Sunshine Tidings from Preston and got the Settlement as well. Due to the fact that the build areas between CAS and Build High are different, i had to scrap a few things more, everything fine. Flying worked, Scrapping works, Undo works.
4. Got Greygarden quest, but hadn't finished it at this stage.
5. Went to build up Sunshine Tidings and Starlight, Starlight will be quite beefy with about 30 plots, mainly commercial, recreational, 3 martial plots and including 5 additional residential plots. Gives me a total of 27 possible settlers with some other jobs and food production. Did that before and it worked without major issues apart from some minor performance impacts and FPS going down to 45-50 FPS at some times, generally it was around 55 FPS.
6. I started with Starlight and suddenly flying wasn't working anymore after i set the SimSettlements plots.
7. Went to Sunshine Tidings. Flying there worked. Did set a total of 6 plots, exited Workshop to save, wanted to re-enter the Workshop mode, flying not working.
8. Tried the sprinting suggestion from a user here, not working.
9. Out of habit i start the Workshop mode always with the V hotkey and didn't set any Hotkey for the Workshop Lag fix. It is a bit like Todd Howard, it just worked so far
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10. I tried pretty much everything. All settlements without a single SimSettlement plot work fine. As soon as one plot is set, flying stops working. Not completely, sometimes it is OK, but it is not reproducible, for example that you could say after fast travel it doesn't work or after a virgin was sacrificed by moonlight.
11. I looked through my entire load order and noticed Workshop Lag fix, a mod that you usually never think about unless you fall over it. Went in-game, opened MCM and don't know why, assigned a hotkey to start workshop mode instantly. Saved everything to have a base line.
12. Went in-game, walked to Starlight, started Workshop mode with V, no flying, repeated that with Sunshine Tidings, no flying. Repeated everything just this time with fast travel, again no flying possible. Repeated everything with opening workshop mode, closing it and repeatedly opening and closing workshop mode. Sometimes i could fly, but i would roughly say out of 30 times it worked once, if at all.
13. Repeated above, just this time i used the hotkey from Workshop Lag fix, and behold, until now i could fly each and every time. As soon as i open the workshop with V flying doesn't work.
To me it seems the flying functionality from WS+ doesn't get aware of entering the workshop mode if the lag fix is active and you use the normal method to open it. Only when using the hotkey from the lag fix it notices that you entered the Workshop. How the relation to SimSettlements fits into this i can't explain tho. I only know that the problem occurs only after the first plot is put down in a settlement, no matter what plot type it is.
The next thing i try is to actually disable the Lag Fix alltogether. But as testing takes quite some time i will do it over the next two or three days. If anything changes i will certainly post an update, otherwise assume that the Lag Fix is causing the issue and try yourself if you can replicate my findings. If yes we found the guilty party and maybe kinggath and registrator can put their heads together to find a solution.