what i am about to suggest i have tried it once, with success - but as it has been a while, i could have forgotten something or something could have changed until now. Anyway:
savegame folder -> mods.json
open with text editor.
add/remove the mods you want within that file
It could create problems with objects/monsters/locations depending on the mod. It may also work fine.
PS. that’s for the ‘official’ mods. for the unofficial ones (those that require using external data besides the main catadda files), you should go ask in the mod’s thread.