I had the same issue i have 263 active plugin and FS4E sim settlement and scrap everything the problem come from 3 mods together or perhaps the interaction between them.
So like when i install i mod it can make FS4SE doesnt launching the message fallout 4SE its not correctly installed after that i load the save and bam naked personnage quest reset and all modded stuff gone.
So again like save bleed bug and luckliy if i save enough i can still save half the character it happened a few weeks again when i wanted to install a ammunition mod Professionnal ammuniton crafting (PAC) the mod at first didnt make the famous F4SE bug but after i quitted the game and relaunched i had the F4SE message.
So i lose my character level 60 and i had made a few save so the last good one was the level 30.
I use nexus mod manager and no i dont use tool to sort my load order at first i just installed mod without checking.
Anyway after that i reinstalled all mod and sorter everything myself in a logical sequential fashion :
First heavy scripted mod and overhaul sim settlement radstorm etc...
After aesthetic mod cbbe etc...
After Power armor
After armor mod
After that weapon
in the last scrap everything and the vault 88 crash fix that must be a culprit for the problem.
It helped but i did remove a lot of save fo be sure.
I had a character level 120 but its gone.
I know that i need to remove scrap everything but the game design in settlement is to horrible and unless i find a mod that remove all building in settlement i will never build in those ugly place
I am sorry i am dont have any solution to save character save i tried falrim tool to no avail.
I guess you cannot salvage a corrupted save first fallout 4 save system is defaillant in is vanilla form so if you add mod it make the thing more complex.
Now when i install a mod i make a few extra save to be sure to lose a minimum of level and sutff.
Its a band patch but so far it work if i install a mod that make the game reset everything i just remove it and lose 2-3 save point because of the bleed save bug