That is the way auto import feature has been designed.
It just keeps an eye on the watched folder and moves the images from that folder to the destination location that you choose in Auto Import settings while importing them in Lightroom: Auto-import photos into Lightroom
But why you changed it the LR file?
We can not tell him that the source and destination folder is the same (that we can) and it does not copy constantly identical files (it's not very logical)
Then configure LR to move the files into the FTP folder, not from it.
This is not necessarily perfect but I test.
Otherwise called me which file to edit it no longer deletes the file data.