Turn off Replace ‘\:*?’ option in transfer settings:
https://beta.winscp.net/eng/docs/ui_transfer_custom

We've been doing a sync of a large folder and have had several files fail because they couldn't be found. Come to find out, the filenames were something like Sample%2 File.pdf. WinSCP seems to choke whenever there's %(number) in the filename. It appears to try to resolve the ASCII value.