Both windows and linux have temporary directories to download to prior to replacing a mod. The environment variables to try are TMP_DIR, TEMP & TMP (in that order I believe).
The reason for this is that I've had plenty of occasions where the mod manager removed the old mod but failed to fully download the updated mod, leaving only a skeleton mod that is recognised during boot of the game but causes it to crash when attempting to play because it's missing key data files.