I reckon you are talking about Zebra VC80X device.  Most  brands of Android devices will have the device agent and all installed apps intact after firmware update.  One of the exceptions are Zebra devices.  Unfortunately, I don't have access to any VC80X to do any tests, so the following is just my educated guess based on previous exposures to other Zebra device models.  

Zebra seems to include an "enterprise" partition on most, if not all, of their devices to store important system apps such as MDM device agent and important enterprise data.  This partition remain untouched even if the device has been factory reset.  A separate command is used to reset/clean-up this enterprise partition.  So, if your your device agent has previously been installed here rather than on the normal partition, you should not have problem even if you use file-sync rule to download some kind of flash image to the device for subsequent flash/firmeware update using Zebra proprietary upgrade procedures.  Please check if this is the case on your VC80X.

Here is the way we have been successful.  If you don't do all of these steps I have seen weird things happen (Like using Velocity app the font size doesn't match and enrollment fails over and over)

1. If Soti Mobicontrol shows that it's enrolled - hold down on Enrolled to unenroll.
2. Uninstall all Soti Mobicontrol by holding down the app icon and choosing App Info then unenroll
3. Insert USB key to PC and copy all files to the root of USB:
   
   
   1. 1 ATLAS_N_ENT_RESET_AOSP_01_49.zip - Enterprise Reset
   2. 2 ATLAS_N_FACT_RESET_AOSP_01_49.zip - Factory Reset
   3. 3 VC80xU10.upl - Scripted update - contents of file are :
      package:FPU_ATLAS_02-32-04.00-ON-U00-STD.zip
      package:CFE_ATLAS_02-32-04.00-ON-U01-STD.zip
      package:CFE_ATLAS_02-32-04.00-ON-U20-H16.zip
   4. FPU_ATLAS_02-32-04.00-ON-U00-STD.zip - Full 8.1 upgrade
   5. CFE_ATLAS_02-32-04.00-ON-U01-STD.zip - Mandatory update
   6. CFE_ATLAS_02-32-04.00-ON-U20-H16.zip - Delta update
   7. VC80xOSU10Update.xml - Update XML that is read by scripted update file
      <wap-provisioningdoc>
        <characteristic version="8.0" type="PowerMgr">
          <parm name="ResetAction" value="8" />
          <characteristic type="file-details">
            <parm name="ZipFile" value="/sdcard/VC80xU10.upl" />
          </characteristic>
        </characteristic>
      </wap-provisioningdoc>
4. Boot to recovery
   1. Reboot device by holding power and choose restart
   2. Hold (volume + and POWER) until you see Zebra logo
   3. Let go and you will be in Recovery mode
5. Use plus/minus to browse Apply upgrade from USB drive file and power to select.
   1. Install the following 3 updates
   2. 1 ATLAS_ON_ENT_RESET.zip - Enterprise Reset
   3. 2 ATLAS_ON_FACT_RESET.zip - Factory Reset
   4. VC80xU10.upl - Scripted update
6. Choose Reboot System Now when done.
7. After upgrade, you will have to re-enroll the device 

Hello Charles,

Thanks for your post!

Have you gotten a chance to try the above suggestion made by the community? If not, let us know if you are still having difficulties.  

Regards,

Technical Support | SOTI Inc. |1.905.624.9828 | support@soti.net | www.soti.net |