I'll explain how it's supposed to work.
After the encoder2 switch is pressed for 2 seconds, system enters in color update mode. With encoder 2 you will be able to create a custom color and with encoder1, using a flag named colorUpdate you will update the LEDs brightness. Once you get desired brightness and color, you will press the button again for 2 seconds to exit the mode (this done with the flag activation = true/false.
Using the encoder switch should work like the button you suggest.
On the other hand, I can't do it make the changes after a inactivity, just because there's more code and the encoders are intended to have other functionalities if colorMode flag is not active.
I can share the whole code so you could understand better but it's still in developement and not complete. Would you understand better with it, I have no problem posting it.
All of this was done using the methods provided by Neopixel library, in case I updated it to FastLED those brightness() and checkColorMode() methods both might change.
A risk of missing something unless you alos add the Hail Mary pass to EEPROM as power sags. As for that, sorry I didn't fully understand.