That does sound like quite the tangle. 

I’ve done one upgrade so far and let the console handle it. On version 24.2.3 there wasn’t a way to control the deployment via SCCM unless you did an uninstall then install (that would be a great feature, by the way). I think I remember reading in the change logs that they made some very big changes to the jump client and even had some bugs, so you maybe that is what you are running into. 

What comes to my mind (apologies if some sound very obvious): 

1. Do you have an old deployment for an old version of the jump client? I’d update your deployments to only use the new version
2. Enable debugging logging to see if it’s giving any additional info
3. Run the items by hand to see if more descriptive error messages are given
4. In your Rep Console, try to right click and uninstall or upgrade (though it sounds like they are already pending) and then start the service to see if it’s online long enough to get that command from your appliance
5. Do a clean uninstall then install of the new version
   1. This is what I have for an uninstall, note, we are on version 24.2.3: 
      1. c:\programdata\bomgar-scc-*\bomgar-scc.exe -uninstall silent
      2. Then I go and do a basic msi uninstallation of “Remote Support Jump Client*”

Hope that at least gets you going in the right direction. Good luck.