I found that deactivating mods caused problems. I instead use the restore function of FLMM, that seemed to resolve all problems with reactivating/deactivating mods.
<span style="color:#FF0000"><strike>RETIRED</strike></span>
ON MY WAY OUT OF RETIREMENT
You might have corrupted your game folder by deactivating the mod instead of restoring backups. Try hitting Restore backups now. If it doesn't work, reinstalling is your best bet.