Refinement flags are not persistent in state save

[joelvbernier]

Upon reloading a state, any parameter refinement flags are all set to False, regardless of their value during state save.

GUI is current master.

hexrdgui                  0.8.16.dev66+g18f5ba4           dev_0    <develop>

[psavery]

Looks like this is related to the fact that we are writing/loading the instrument config via HDF5 instead of through QSettings (see it being skipped here.

I think we can add an extra step in the save/load methods to include the refinement flags as well.