Removing mods with modded saves

[StaticNebula26]

I want to cull all of my mods and then reinstall only the ones I’m using in my ships. Is this possible without corrupting my saves and more importantly my craft files?

[Gargamel]

Make a backup of the GameData and Saves Directories first.   That way, if it goes sideways, you can just drop the entire thing back in place. 

Why cull all of them?  If you know which ones you want to keep, just keep those.