Hi dean,
thanks for your question!
Applying the scale works by pressing the two buttons “Midi CTRL Alpha” and “Midi CTRL Beta” in Global menu. The scale does not get reset to chromatic automatically after applying the scale, it has to be done manually.
The scaling feature itself works by looking at the notes just before they are being played out and moving these onto a scale without altering the underlying note info.
What happens underneath by applying the scale is that the note values that are in RAM are really being changed according to the global scale that is selected at the moment.
You then can make that alteration permanent by storing the pattern in flash.
After that it´s recommended to turn off the scale setting in Global menu to prevent the note from being scaled again (it was already scaled by applying the scale).
If you would apply the same scale it wouldn´t matter, but for different scales it might be undesirable.
The workflow was intended so that if you plan to use different scales over your patterns, you would individually apply them to every pattern and then turn off the global scaling (= chromatic setting).
Please let me know if you have more questions in this regard.
Cheers!