Just a tiny update on the situation in case anyone else has to deal with this, I am sure this is an UE4 problem more than anything, but I fixed the corrupted struct and used soft object references in the struct, still was having crashes when saving the game, even after deleting the save files.
I managed to understand where the issue was after quite a few hours of testing, when I used the “Remove” node on my map to remove an element from the map then pressing save, the game crashed, even if I gave it some time before saving. Instead, I stopped using maps and resorted to array of structs and all started working fine, no more crashes!
Using “Clear” on the map didn’t cause crashes, but “Remove” did.
This only happened to maps that had a key of string, name (and other primitive types) and value of structs.
Hope this helps someone, sometime