Can’t sell the gold to the commodities market

I can only definitively answer part (1), and that answer is:

Yes, once you have explored a system you retain that information and it shows on the System Map for you.

I understand from the game forums that the first players to survey a system get more income from doing so than later players - but that later players do get some (presumably this data is confirmation of the earlier surveyors' findings).

I recall from memories of statements by the developers (can't cite, sorry) that in the released game, systems that have been explored and see a lot of player traffic will eventually have space stations built and come under faction control. I don't know whether the faction that players sell the data to has influence on the faction that moves into the system.

Still no idea of the cause specifically, but I have found that the following will allow me to continue mining without restarting the game....

• After the glitch occurs, shut down power to refinery (glitchy noise and msg should have stopped)
• Supercruise outside current location, even if it's only for a second (refinery hopper should be empty after you get in supercruise)
• Turn refinery back on while in supercruise (glitchy noise and msg should not continue)
  • Empty a bin from your refinery, just for good measure. Not sure if this has an affect or not, but I do it every time.
• Supercruise back into location / drop out of supercruise
• Perform "Reboot and Repair" in System > Functions menu

After reboot of ship systems, refinery should be online without glitch, and will accept fragments again without triggering the glitch.

This has worked for me three times in a row, hopefully it works 100% for everyone else.