No. The PDP app will track per diem until it is told not to (by selecting "No" on the Trip Notification). Once you select "Yes" (and you do need to select Yes at some point if you want per diem tracked) the PDP app will sync the tracked data with the web server and continue tracking the per diem.
Note: If you transit your tax home halo the app ends a trip, but posts a new Trip Notification alert when you depart the halo. Confirming the Trip Notification overrides the trip termination while transiting the tax home halo.