From what I remember, you WILL lose your trigger settings and everything, along with your custom kits, when you reset to factory settings.
I had to do this once a couple years ago, and I went through all my settings and recorded the values that I had set. I did the same things with my custom kits. It can be time consuming, but if you just snap a picture of each relevant menu page, it makes it so much easier to go back to the settings that work for you.
It took me some time to get everything set back up, but the factory reset was worth it for me at the time.
EDIT: After I made that post, I remembered something. I seem to recall that you can back up and dump your trigger settings file via the USB cable? Someone can correct me if I'm wrong, though. It was something that I think I saw AFTER I had done mine. However, with the issue you're having, if it's something that's corrupted the settings, it may be better to manually reset everything, or you could end up with the same problem. That's a guess on my part. I usually only have about 4 or 5 kits on my module that I really don't want to lose, so I'm more of a "do it the hard way" kinda guy, LOL.
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Shawn.