I tried again with the daily build ISO from today (March 1st) and can confirm 
it is really the boot entry, which is corrupting the configuration file.
Once the boot entry was created by the installer, the configuration was no 
longer readable by Hyper-V, removing hte ubuntu entry from UEFi with efibootmgr 
restored the configuration files again.

So we must find out how the UEFI boot entry can be created without
breaking Hyper-V.

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https://bugs.launchpad.net/bugs/1272664

Title:
  Installing UEFI boot entry on Hyper-V gen 2 corrupts VM configuration,
  making the VM unuseable

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