If a mod's file .zip is in use when you try to delete the mod from within the game's UI there is a crash message and the game restarts.
I had a json file open in a text editor inside the zip that I forgot was still open when I deleted the mod.
Game crash when deleting mod (0.13.20 24011 W64 Steam)
Re: Game crash when deleting mod (0.13.20 24011 W64 Steam)
If it crashes then please post the log.
Re: Game crash when deleting mod (0.13.20 24011 W64 Steam)
Should be fixed in 0.14.10.