The issue is the BizTalk 2020 SFTP receive adapter does not delete the SFTP file after downloading it from a MoveIT SFTP server.
This issue has already been reported but I cannot find any resolution on-line yet:
https://winscp.net/forum/viewtopic.php?t=29529
Apparently it's an issue with different timestamps being returned from the stat and ls commands from MoveIT SFTP servers:
I am thinking of writing some C# code to manually delete the file as a temporary work around.
However, I would like to know if there are any plans to fix this issue in a future BizTalk Cumulative Update?