it happens when you load a saved game. you lose perks and all progress but keep inventory.
Note that some perks reset every night (The same time you save your file)
I had best friends, working boiler, workiung atenna and liberation militant. Those were all gone after I saved after fighting cody. Even editing money in the saves got reset.
Can you send me those save files? retsymthenam@gmail.com
Sent them.
when i load save i lost all quest proggresions.
