An ESE backup fails with multiple errors "InstantData stub file - modified".
This is most often caused by antivirus activity.
As part of the archiving process, stub files are created to link to your actual data that is stored on our platform. When you access a stub, the data is automatically downloaded.
What happens here is that the ESE agent scans the disk to check which files (including stubs) have changed since the last backup. When an antivirus product sees the agent accessing a stub, it runs a quick check on that stub to ensure it is not doing anything malicious. This partially rehydrates the stub. If the partial rehydration happens between the initial scan and the point at which the agent tries to backup the data, the scanned data does not match what will be backed up, resulting in a "stub file modified" error.
The best solution is usually to put antivirus exclusions in place, as listed here.