The refile_part utility has an option for part cleanup; but the automatic cleanup is fairly limited compared to the options offered in interactive NX. Alternately, you could create a journal of the part cleanup options that you want. If you have an author license, you can compile your own .exe for a "batch" run. If you do not have an author license, you can use the run_journal utility to get a similar result. However, the journal code (wheter run as a journal or compiled to .exe) will require the use of an NX license while it is running.
I'll look into trying those. I haven't used the run_journal utility or built an NX open application so I'll need to read up on how to get that created. Thank you all for the advise.