Removing multiple machines at a time.

Why bother removing them? You should never really have a reason to delete a
system from the JSS until the system is no longer something you're managing.
The only situation I come across as a precautionary measure and would remove
a system is when it might move from our Labs area to an Office area, but
really I just want to ensure any autorun data is deleted for any box in our
offices side so something bad with a system imaging itself somehow doesn't
happen.

To your question.

Update the name on the machines themselves and run a Recon cycle either on
the machine or as a batch using Casper Remote, and it will update the record
automatically in the JSS. If you are doing scheduled recon inventory cycles
the issue will clear itself up.

Or reverse that, if possible, and update the names in the JSS and run a
policy or remote session to reset computer names from your JSS records. The
catch here would be to ensure the reset computer names happens after you
have updated the records in the JSS and before any other recon cycles
happen. If a recon cycle happens before the reset computer names runs, the
recon will update the JSS record with the current name again.

Just my opinion. Let us know if there are more questions.

Craig E