If the FC fails to boot, it will come up temporarily with a set of default settings. The old settings are still there as long as you don't save settings over the top of them.
So I think the way to attack this is to find out what causes the "won't boot" with your settings issue.
First of all, if you power it with USB do you get the "real" settings? How about when you add flight battery power after booting with USB?
If you can get it to boot with settings with USB, do an export of those settings if they are newer. You may want them later.
If it boots correctly with USB, but not with flight battery, be aware that flight battery also gives power to plugged in devices like the receiver, but USB does not give power to those. Try unplugging things to find out what it "doesn't like" when powered with the battery.