Weren't the skipped files added while WinSCP was running already? To investigate, please add dir *.xml before and after calling WinSCP. If you want us to check, post an output of your batch file, as well as WinSCP session log file.

In case it turns out you need transactionally-safe move, see
Moving local files to different location after successful upload

HI everyone,
Hopefully someone can help guide me on this.
We have a script we run as a scheduled task every 15 mins which copies files to a SFTP location, then after this a move command to keep a copy of the files locally.
For some reason it keeps skipping a few files each day which are not uploaded, but do seem to be moved via the move part later in the script.
We upload every 15 mins, and each batch would have a max of 20 files
The part of the script used to copy the files to the SFTP location after logging in, and then move so we have our local copy is as below:

Can anyone suggest why it may skip the occasional file in the put part but the file is successful moved to the backup location,
Many thanks in advance.