I just did this upgrade on Friday, and used the Nortel upgrade tool. I've done lots going to 4.x and 5.0, but this was the first 6.0.
After going to 6.0, about 20 of the 65 sets had changed DN's. Set relocation had been in use for quite some time, and very few of the port assignments were default before the upgrade.
After 2 hours of changing DN's, all was o.k.
All of the programming was retained with the upgrade. All of the target lines were changed, as were the analog trunks. The only problem was the glitch with the DN's