Any change (idle speed, timing, whatever) requires a re-program/re-flash
Basically, you:
Connect to OBD2 port, and on the XCAL2, Select "Program". Select the Tune you want to use.
The next screen is where you hit select to make changes or hit cancel to just do the program with the settijngs in the unit. Hit select then scroll thru the options you want to adjust. When you are on idle speed hit select then arrow to adjust, thens Select again to accept...at the end you hit cancel to go out...note that the tune you have must allow changes for this to apply.
Then Start the re-program/re-flash
and getting back to your original question, the changes you make seem to be stored on the unit itself....since after changing timing, when I wanted to go back, they were still there in the unit.