FTP servers may restrict number of files returned in a listing
If you upload a large amount of files (typically several thousand) to an FTP server (especially if all in one folder), you may find that the next run of the profile suggests re-uploading many of the files you thought had already been transferred (and which the profile's log of the initial run also show had been copied already). The profile will act/display as though those files do not exist on the FTP server.
This may well be due to artificial limits set by the administrators of the FTP service (and/or, the default configuration of any such FTP server software) as to how many files it will list. A favorite number seems to be 2000 files, as shown here.
Note that any listing will likely include the standard . and .. directory entries, so if the limit is 2000 entries, you may actually see a listing of 1998 files (or similar)
The only cure is to arrange (request?) that this limitation be changed or adapt your storage plans to suit. Otherwise the profile will continually upload files that are in fact already there, but which are just not being listed.