What protocol are you using? Do you know if the protocol allows changing those flags (I wouldn't expect that).
Anyway, you might be able to define a custom command to manage those flags.
https://winscp.net/eng/docs/custom_command
Or even implement a WinSCP extension.

I use WinSCP to manage FreeBSD systems using the UFS and ZFS file systems. I would like to be able to edit and view file flags using WinSCP instead of having to resort to the command line.

File flags are described here: https://docs.freebsd.org/en/books/handbook/security/#security-file-flags