I had the MFDeploy tool connected during the application update, it’s there where i had this message, and from there i was able to manually deploy the application hex file again.
The application itself checks at startup if there are firmware updates on the SD card, i true -> start update proces.
Root of the problem was caching, this how it was done :
//download files over FTP to SD card is done, reboot the device to deploy this
And this is the fix :
//download files over FTP to SD card is done, reboot the device to deploy this, but flush and wait a bit before rebooting...
I did like 100 upgrade / downgrade cycles today with this modification at a 0% fail rate