If you have fully transitioned to DEVONthink 4, including activating a seat for the machine, you should remove version 3 from at least your user account on your Mac to avoid confusion. You should not have version 3 and 4 on the same account, on the same machine.
At a minimum, you can delete the DEVONthink 3 app from the Applications folder and reboot the machine. Note: You may need to quit Safari first as our browser extension may be loaded and in use.
For information on doing a deeper clean, please contact our support.