@ctarbox How are you scoping your Configuration Profiles? If they are scoped via a Smart Group any change that causes them to drop out of that Smart Group will trigger removal of the profile. If you've got EAs that are used as Smart Group conditions I've seen instances where the EA data "goes missing", and comes back on the next recon, so check those if you have any.

I've had this same problem with M1 Macs running 11.3.1, the configuration profiles from the Defender for Mac and the Classroom Configuration all disappeared. These profiles are scoped using a static group. I'm running Jamf Pro 10.27 so not sure if an update to 10.28 should solve this issue. But any suggestions from fellow users would be welcome!

I'm experiencing the same issue after upgrading to Big Sur, are there any updates to this issue?

All Config Profiles except the main MDM Profile will go away

Have the same issue here as well with an M1 MacBook Air running 11.4

Was doing some testing, logged out of the user account, and lost all 22 profiles except the MDM profile. 

The only thing that I have found that fixes this is to assign or unassign a device owner. Profile come back immediately. 

Has anyone found a solution to this problem ?

I have opened a ticket with Jamf and it sounds like it is a known issue on Apples side.  There is an open ticket with Apple on this issue

"where this happens after LDAP logins for our AD Bound machines where Configuration Profiles can be removed"

I have rolled all of my machines back to Catalina

Fast response much appreciated.

I’m seeing this on 11.4 which I know is old (limited to support some Avid software. I presume the issue has been seen throughout Big Sur versions 

Hi, just encountered this issue here as well. Machine was on 11.4. We updated it to 11.6, re-enrolled and only 3 profiles besides the MDM profile reinstalled. We had to exclude the computer from the configuration profile deployments, then remove it and they all showed up again. 

Did anyone ever figured out why this was happening? I'm having the same issue on Sonoma 14.6

Can confirm that this is an issue in our computer labs running macOS Ventura. Unfortunately, the only workaround I have found is to reinstall OS and not sure how long that will stick since its technically the same policies and configuration from before. Any actual fix for this would be great as its interrupting instruction in our classrooms.