What I did was to remove the nut and replace the seal and then replace the nut back to it's original spot by lining up the stake marks and then staking it back down in it's original place. Probably not the ideal way of doing it but it seems fine after 6k.
I replaced my rear oil seal this evening and the above advice worked well. However, I made some mistakes and I'll pass the hindsight on.
I can think of three things I did that were good (not many, I know) (1) The first was to make some reference marks to relocate the position of the nut. With everything still tight, I took a Dremel (an engraver or scribe would work just as well) and placed aligned marks on the stake nut and the shaft to precisely locate how far the nut was threaded on (in case I ruined the stake nut and lost the reference). (2) Before breaking into the third member, I spent a good while twisting the companion flange by hand and getting "a feel" for how much preload should be on the backlash (I do not own an inch-lbf torque wrench) (3) When I ordered the oil seal from CDan, I got an extra stake nut, just in case.
Firstly, I tried a bunch of chisels and punches to "undo" the stake nut, but didn't have one of ideal width. So, I tried a screwdriver. I chose a cheap one as I was going to ruin it anyway; this was a mistake. I broke the brittle blade of the cheap screwdriver off in the crevice between the stake nut and the bed of the keyway. This added some time and I screwed up the stake nut so bad in the process of getting the screwdriver blade out that it was unusable; not what I had envisioned.
After replacing the oil seal (by the way, if you've done the birf job and have the 54mm hub socket, it works mildly well to press in the new seal), I used the origninal stake nut to push on the companion flange until the Dremeled marks aligned. At this point, everything is in it's original position, but I screwed up the stake nut so badly that I couldn't stake it. So, I removed the original stake nut and replaced it with the new one (by the way, the old stake nut sat on a separate plate washer; the new stake nut has a washer built-in; so, with the new stake nut, I didn't use the old washer), snugged it up against the companion flange and staked it down. Again, I spent some time twisting the companion flange by hand and it felt the same as it did before I messed with it.
So, I suppose the my advice would be to:
(A) Add some clear reference marks to realign the stake nut with the shaft.
(B) Take care in "unstaking" the nut so that it can be reused and find the proper tool to do so.
(C) Have an extra stake nut on hand just in case (they only cost about $3).
EDIT: My seal began to leak when I went to synthetic diff oil. It's had been slowly leaking for about two months and lost over a quart of oil in that time.