If I install version 5.5.3, will all my batch script commands work the same?
Yes, in 99% of the cases.
You can search version history for "Change:" to find all backward-incompatible changes.
https://winscp.net/eng/docs/history
https://winscp.net/eng/docs/history_old
Though the script shown about should not be affected. It uses some obsoleted syntax (like
option transfer ascii
), but all of it is still supported.