Since you've set it up to overwrite the file on every upload then technically yes, it can delete the file it uploaded. The FTP server's actually doing the deleting - any time you upload a same-named file (with AbelCam or anything else) what's really happening is "delete the old file, now here's the new one to replace it". So if the transfer fails at a certain point then a file that seems to disappear is not impossible.

There have been some problems with FTP in recent versions of AbelCam. There is lengthy discussion of it in THIS THREAD on the Issue Tracker. Most people have reported corrupted image files but depending on your FTP server it's certainly possible that missing files could be a symptom of the same issue.

The best I can suggest is to edit AbelCam's CONFIG.XML file: find the line that says "ChilkatFTP false". Change it to "ChilkatFTP true" and see if things improve.