I understand, but my original answer still stands; there is no way to
automate this.

From what I understand from you there were certain users who directly sorted
their mail via rules to a pst-file you consider as an archive instead of
sorting it into their current mailboxes. That is what created the issue. If
they sorted within their mailbox with rules and archived to a pst-file via
the archive feature you could simply disable the archive feature (as you now
have server-side archiving) and be done with it. It is the mix of using
rules for both sorting and archiving that created this mess.

I assume that the imported pst-file isn't just to be left there in the
mailbox for eternity? This has to be integrated with the mailbox, project
folders or corporate knowledge base, right? Otherwise your users would still
be archiving manually within their own mailbox which is what you don't want
anymore. Or has this pst-file been merged with the entire mailbox instead of
put in a separate folder?

The solution is that they reevaluate their current sorting methods to the
changed environment. This will probably mean that they can drop a lot of
rules instead of translating them 1-on-1. They can now take much more
advantage of other sorting methods such as Search Folders and custom views
since everything is now within a single mailbox container instead of mailbox
and additional pst-file containers. Rules will now also be server-side
instead of client side which is another modification needed to the rules.
Yes, it will take some time now, but ultimately it will increase their
productivity which is the main reason why you implement IT systems.