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As you may have discovered, hopefully not the hard way, many backup tools (CrashPlan in my case) will only backup a VeraCrypt encrypted container when it is first created or seen. This is because the encrypted containers ‘last modified’ timestamp is not updated by default when you make changes to your data.

To resolve this, simply open VeraCrypt and navigate to ‘Settings -> Preferences’ and disable the ‘Preserve modification timestamp of file containers’ setting.

Disable "Preserve modification timestamp of file containers"

Keep in mind that backing up large encrypted containers this way is extremely inefficient. Changing even a single bit in a 5gb container will force the entire 5gb container to be backed up again.

If it’s important enough to encrypt, it’s likely important enough to back up! Don’t be caught off guard!