It sounds like you're using a prestage enrollment with your DEP iPads, so I'll go from there. There isn't a way to automate the re-enrollment of non-DEP devices, but you can automate profile and app installations once they are re-enrolled by creating a smart group to catch these non-DEP devices and scoping the profiles and apps to that group. You would still need to use AC2 to enroll them, but this takes some of the work out of the process.
Of course, the cleanest solution is always to bring the non-DEP devices into DEP so they can leverage the prestage enrollments, but I know that's not always possible.
As a side note, have you created a supervision identity to share between Configurator 2 and the JSS? It's not essential by any means, but it does mean that all devices, regardless of how they get surpervised, are supervised under the same identity. You can create the identity in either platform, and then import it to the other. You can check the admin guide and this technical paper for more detailed help.
@bburdeaux thank you for your response. You have confirmed my thoughts.
If I may ask, how could one bring the "non-DEP devices into DEP"?
@ruschg If they were purchased directly from Apple, they can be imported in the ASM or ADP portal, by serial numbers or by order numbers. Over the last year or so I've managed to get a large majority of our older devices into DEP, mostly just using either individual serial numbers, or .csv lists of serials. We've always bought everything direct from Apple, so I don't have any experience with this, but there are some cases where devices bought from resellers can be put in DEP as well. If that is the case for you, I'd ask your Apple rep for the specifics.
@bburdeaux Brillant - just found the link in ASM. Thanks a bunch!
