No, you should not change AppID allow list and EWSEnabled at the same time. Again, I suggested exact steps with a reason; you want your results to be predictable and control exactly when settings will take place. Allow 24 hours for AppID allow list setting to sit. Then choose the time when you want to flip EWSEnabled to True and know that you will see results in max 1 hour. If you changed both concurrently then you are not quite sure when both things will take effect and you might find yourself in a situation you did not expect.
If things are not working, you need to figure out what was wrong and fix it and test again (if you need to put any apps on the allow list). And yes, before October comes around your EWSEnables should be set to True, if you need EWS to keep working, as starting October, we will start to flip any EWSEnabled from Null to False. So unless your EWS Enabled is set to True, we might disable your EWS then.
(I'll make a few tweaks in my original reply above to clarify)