I recently went through the same migration. It went really smooth, it was almost scary. My contigency plan was this way. I was going from Netware 5.1 and GW 5.5.5 to Netware 6.5 and GW 6.5.2.
My procedure was as follows:
shutdown all gw agents and make a full backup to tape when that finished i ran a backup to disk as well. Because I had read that sometimes db files even when they aren't accessed have issues. I then copied gwpo.dc, gwdom.dc, mtaname, wpdomain.db, wpdomain.dc, and wphost.dc to my usb flash drive because I am completely paranoid. From there I reinstalled Netware, and then GW.
I copied all user db's, domain db's (the entire domain structure to the new box) and did an in place upgrade. One thing that was not mentioned in the guide was I wacked the following objects out of my tree (gwia,mta,webaccess) DO NOT wack anything else.
It worked like a champ. All of my users maintained the same 5.5 FID that they had therefore if you have archives you do not need to do anything to them they will be ok.
As far as fallback plan....make sure you have a complete backup of your GW 5.5, also I recommend buying Portlock Storage Manager. It is basically ghost for real OS's.
I hope this helps out.
Tamra Graver --CNA, Network+
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It is my job to comfort the disturbed
and disturb the comfortable..........