Don't know what happened, it was there yesterday and today after doing the upgrade it's gone. Other saved run configs are present, but that one's missing. Quite annoying since it had a bunch of config in it.
I have most of config options for dev well documented, so it wasn't a big deal. If you have a lot of stuff in your run config that you haven't got documented or backed up, might want to do that before upgrading. I also found a log statement in the idea.log file that contained the settings too, so you can try looking in there if you're missing some config.