Right now, your “personal” game info gets stored in My Documents—deployments, ship designs, etc. If you swap mods in and out, you have files put there that the game cannot work with when the mod is gone, and it crashes on startup.
Would it be possible (or in GSB2) to have a txt file that shows a path for all the deployment/ship data to save to. Default is no file, and GSB does what it does now. When someone makes a mod, then the path in that txt file is used instead. If you delete the mod, you delete that txt file, and GSB starts up normally, since ALL designs, etc, made while the mod was active are in a folder GSB doesn’t look at.
Using JSGME, you’d swap that txt file in and out, so when you uninstall the mod, GSB is untouched, vanilla (with official GSB content add-ons, obviously).