For USMT, all the Code42 app does is call Microsoft's USMT, has USMT save the .mig file in a folder we back up, and then back up that .mig file. The Code42 app can restore the .mig file back to the device. After the restore, Microsoft's USMT tool takes over and handles the .mig file to complete the migration. The Code42 app doesn't really have anything to do once USMT takes over.
The Code42 app shouldn't be doing anything special, or unusual, to the .mig during the backup, or the restore. The USMT .mig file is just a file, like any other file. They found several results that indicate USMT can cause issues with O365 even when the Code42 app is not involved. Below are examples of a web search for USMT causing office 365 issues:
Two of them mention something about needing to disconnect the O365 profile before running USMT and "unconditionally excluding the AAD folder from local Appdata"
Given the findings that USMT can cause issues even when Code42 is not involved, it might help to have someone test a USMT migration without using Code42. Create a test device that has an O365 set up in a way that mirrors how an end user would have their device set up. Next, you could use USMT (without Code42) to save a .mig file to a thumb drive, or some type of removable media. After the .mig file is created, wipe the computer and try to set it up again using the .mig file. See if the issue happens again.