I had an issue this morning where a couple of drives "failed" -- after reviewing the data I determined it was likely related to a connection issue and not the drives themselves (all drives related to the connection were throwing read errors). I then:
- Stopped the array
- Removed both drives (one of which was Parity 1 of 2)
- Started
- Stopped
- Added both drives back in
- Started
This is where things got sketchy.  After having replaced the cable, one of the other of the drives that was having issues then disconnected.  At this point I'm aware something is still unstable in the system hardware somewhere.

At the same time though I was trying to remove one of the drives from the equation because it was empty...so stupidly I:
- Stopped
- And....created a new config (again trying to remove one of the drives from the equation to try to help stabilize the situation)

It was at this point I knew I screwed up.

I did NOT start the array with the new config.  I quickly pulled the flash drive and downloaded the backup which looks like it was done immediately prior to the new config creation (thank god).

How do I restore the old config?  I see the instructions to restore the flash drive to a new drive but when doing so the system won't boot from the new flash drive.  I have the old USB drive with the "new" config on it, as well as the flash backup downloaded with the known "good" config.  Can I just load backed up "good" config onto the USB drive that has the "new"(aka "wiped") config on it somehow?

The config folder on flash is all you need to get your configuration going again. Possibly all you need is the super.dat file since that is where the array assignments are stored.