After having the file path cannot be more than 260 bytes issue (see previous bug) I substed the folder to a drive to avoid long foldernames.
Then I modified the settings into the drive letter and FTPbox started it's sync. Luckily I had started in debug mode, and suddenly noticed that it started to delete the local files, instead of uploading them to the FTP.
I may have missed some notice somewhere, but... is this default behavior? Or should it have uploaded the files and was it somehow a bug in the application that it thought the files got deleted on the ftp and therefore should be deleted locally too?
Please note that this is quite a big issue - it should warn before deleting files that way, especially when it's so many. In my case I started the FTP-sync to make a cloud backup of my data... instead of that it started to delete my data ;o)