Let me start by saying I am by no means an expert. I assume others will chime in.
I did just finish rebuilding the GM 12-bolt in the 77K10. I did a lot of research to educate myself. So from that I would offer the following.
First, the pinion nut is supposed to be a lock nut. And it is not to be reused once removed. It must be replaced. Otherwise I expect the result will be what you found - a loose nut. So regardless of what you plan to do moving forward, I would get a new one on order.
Second, unless your 12bolt has been converted to eliminate the crush sleeve, then it has a crush sleeve. This means you will not be able to (re)achieve the pinion pre-load again without replacing the crush sleeve. And even with a new crush sleeve, achieving the right pre-load is a bit tricky - especially for us not experienced doing it every day. It is not uncommon to go thru several of them before hitting spot on and not over-torquing (ask me how I know that).
But again, I am clearly not an expert. I would be curious to read what the service manual calls for with a pinion seal replacement. Do they require the crush sleeve be replaced? Just a new lock nut?