The files you get from saving in QGC, should mostly be regarded as a reference, but in case you want to revert to an earlier FW, you should be able to use the "all parameters" files to reload an older set of parameters with that exact FW it was created with, but it can not be used in case of upgrade, because new params gets added with each new revision and the structure and naming changed a few times so far.
So when you upgrade, you need your calibration "params" file and your .mix file with your mixer table and load them in the respective PID and "Setup" tabs of QGC.
For the PID´s, I normally just use the "all parameters" file from QGC as reference and enter the numbers manually after an upgrade. I am not sure if you can add them to params-file as #define´s with the newest revision of AQGC, but maybe you can test it faster than I can, so we can find out if its something we need to work on
Peter can probably comment further about it.
I am gonna rewamp a lot of wikis over the coming weeks, I will go over the parts about parameter to make them clearer.