Clarifications please ... what's the goal? and why backups?
IF Site A (the one where you ran the autobackups) was a older version of Moodle and Site B is a newer version of Moodle and you don't want to migrate Site A to Site B, then choosing the route to restore backups could be an approach.
Just make sure that whatever addons/themes, etc. that was on Site A, have also been installed and functioning on Site B. And recommend not trying to restore course ID 1 from A to B ... that course is the front page of the Moodle.
Before making a suggestion of how one might be able to massively restore backups ... a couple of questions:
1 - the 'other site' you've mentioned ... is it on the same physical server where the backups? or is the 'other site' on a different server?
2 - can you install Moosh and get it to run on Windows?
Of the two questions, #2 is more important but both would have to be known for one will have to use scripts created by you to accomplish what you want to do.
As far as the other problem with users ... since you are on Windows am assuming LDAP authentication is the default. LDAP authentication in Moodle typically doesn't store the password for users in backups. When restoring a course to either different site on same server or different site on another server, both/either would have to have LDAP configured for authentication for the backups to restore and be 'useful'.
Comment: this is really somewhat out of the scope of these forums which explains why you've not gotten any responses to the postings in this thread.
'spirit of sharing', Ken