1) The fact that the AVR returns to a previous configuration after FW upgraded could be related to the fact that they use wear leveling algorithms when they save data to flash memory. Every write cycle to a flash chips adds "wear" to it and after a certain number of cycles (usually around 100000 or more depending on the chip), the data you read from flash is not guaranteed to be right. Since every little setting we change (like last input that returns after power off), we have to write to flash, they might have decided to implement an algorithm that will write the data to different locations of the chip every time they write to it. This way, it is not always the same flash cells that get written to, so it lengthens its life. So say we write a settings block to one section of the flash at the beginning, the next time we will have to write data to it, we will do it a little further on the chip and remember the location where we wrote. The older data still remains in flash but will not be read since we know where we last wrote the actual settings. So basically, the last, I don't know, 10 settings could coexist in flash but only the last one would be valid and used by the AVR. Now if they unfortunately have a bug in their code, it could be that once the FW upgrade is finished, the AVR reads an "older" section of the flash instead of reading the currently used one. This could explain what we observe here.
2) About the Custom Amp assign that makes Audyssey disabled, does it actually prevent you from doing a new calibration? Or does it only prevent you from activating the currently stored calib? If you can still start a new calibration, you will be able to set the amp assignment before hitting start. Then I think it will calibrate using your new config and then let you use it. My guess is that if you change the amp assignment, Audyssey gets disabled so you do not use settings that were calibrated to go with your older amp assignments.