Can ransomware encrypt files within Cryptomator vaults?

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2

This might be caused by one of the following reasons:

  1. The backup programs running in elevated mode: Cryptomator on Windows: Accessing your vault with admin priviliges
  2. They only look through the mount manager interface: Cryptomator with WizTree - #3 by TowerBR

How about you try WinFSP? WinFSP: How to use it