As you may have discovered, hopefully not the hard way, many backup tools (CrashPlan, now Code42) 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.