Kodi deleting files after scanning library

Hi,
I am having trouble (especially with Breaking Bad) where after a scan of the library Kodi seems to be deleting the files. Sometimes it deletes them all and sometimes it just deletes the ones it cannot recognise. After my last scan it left 4 episodes and completely deleted the other 12. Before that it deleted the whole series! I think that was down to the fact the folder was called Breaking Bad Season 5 and it doesn’t like it when you put the season number on the folder name. Why are my files being deleted? Also I can’t confirm this at the moment but I have a suspicion that even though the files look like they have been deleted (they do not show up on my PC or KODI) the amount of space they originally used up has not decreased. It’s like they are there somewhere but I can’t find them on any searches. I am on Kodi 17.1 and Windows 10 32 bit.