This situation happens with Pro-SE regulators as well as Pro-Elite. When lowering working pressure you need to wait till pressure escapes from the regulator. Just make sure to keep solenoid and needle valve open. The best practice is to

• remove bubble counter/tubing from the needle valve
• fully open needle valve
• switch ON solenoid
• now you will see a quick drop of the working pressure 

Alternatively, you will need to wait patiently for pressure to drop to a set level. Waiting time will depend on your bubble rate.