The whole VM backup means that a point-in-time snapshot is taken. With a running database like MySQL this might mean that the database files are in an inconsistent state at the time of back-up. Extra configuration on the Virtual Machine is needed to provide a consistent backup in the form of pre- and post scripts. Microsoft details how to do this in this documentation
That however seems of little use in the situation you are in at the moment. As stated in the InnoDB recovery documentation a good option would be to force manual InnoDB recovery. Documentation for manual recovery can be found here.
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