Hello Dmitri,
The issue of Compute Engine Instances hidden/deleted that you have reported seems related to Compute Engine not Google App Engine.
I would recommend you to create a Compute Engine Issue under the “Compute” section by going here as the issue may be required to refer to the Cloud Engine Engineering team to resolve it. Please select the private component as probably you will have to share project specific information, so that it is not visible to the public. One of the Google Cloud Platform Support Agents will assist you to resolve your issue.
Please note that Google Groups is only meant for general discussion related to Google Cloud Platform products which are not technical in nature, service status updates and release notes, and ranging from book recommendations to creative shortcuts.
Just for your information this document provides information on how to restore a persistent disk from snapshot.