When you install version 3 it duplicates the data store and migrates it to the newer database model. Thanks to APFS this takes only a fraction of a second and also consumes near to no additional disk space. The sync setup is fully moved to version 3 so that there are no conflicts.
You can keep version 2 on the device but its data will not change when V3 syncs. You’d need to set up sync for it again and then sync both generations separately.
When you remove the older version DEVONthink To Go 3 will remove the legacy copy of the data store after a few weeks to make sure it doesn’t unnecessarily use disk space when the two copies begin to diverge.