hi bro,
I think I have found the solution and I hope this can help you.
In my case I used Mod Organizer and it created a new save section in the Documents/MyGames/Skyrim or Skyrim SE folder.
What I did was to copy those saves from the original game folder and those from any other subfolders created by SKSE, and send them to the folder chosen by Mod Organizer ("__MO_Saves" by default).