I noticed that after deleting roughly 500Mb worth of files that were in a folder through the Cloud Manager I didn’t “get back” the 500Mb of space the files were using. Furthermore I checked the local backup of the files and they were still there, but completely hidden if checked in-game. The steam URL for them also keeps working, meaning they were never deleted in the first place.
TTS Mod Manager has a Cloud Tool feature that will let you see “TTS Invisible” files that you can then delete. Be sure to not delete things like “CloudFolder.bson” or “WorkshopUpload”