You know what's really frustrating?

[horndgmium]

When I remove a mod and load a save game, and rather than not load my ships JUST THIS ONCE, when I didn't even click on them, and they don't come back when I put the modded parts back in. There goes quite a large (nice) SS.

I don't even know if that could ever.. not be a thing.

But it sucks. That is all.

[Vanamonde]

Seek (discussion of mod use) and ye shall find (it in the mods affairs sub-forum).

[Mokmo]

backup your saves. Every mod you put in, every mod you take out.

[Rhomphaia]

Why would you think that this is anything other than normal behavior?

If you have a quicksave from before you removed the mods, you can load that after you put them back. but your autosave is gone.