Issue(s?) With Save Files

Hi folks, a few days ago I reorganized all my rom dumps into cleaner folders based on the cores they used, and everything was largely fine at first but after combing through almost all my games I found a fairly odd issue where some cores somehow cannot read the saves at all. I have attempted to look this up online and there’s really not much, the closest thing I’ve found is some desmume threads but it’s not exclusively desmume and it’s not an issue of file types (at least I think not). To even further the issue, I attempted to alter the “sort saves” settings and now there’s multiple saves for games in different places and wiped saves in places where they originally were and it’s become a huge mess. Try to make backups and use said backups has been the worst part here, any backup I place in what I thought was a correct folder is suddenly just not acknowledged by the core in any way. I would be happy to specify more, I understand it’s a multifaceted issue. Any help would be immensely appreciated