As stated in the doc you should always back off data before doing any thing that could jepordise your data. I can never express that enough. Mr Murphy seams to be always setting on my shoulder waiting to jump into the works. At least you were proactive and have all of your data.
Take a sharpy pin and label the drives so you know who who. I'm use to 4+ drives being scattered out and my memory is failing.
If you can get ftp access to the drive you can back that data off where you can read it. If you make a RAW copy of the HD, you can not read the data.
With the set that does not have data, use the drive utility and change it back to JBOD. easier than using debug.
Now run co de info and print it out. for reference
Now Install the Original HD in what I call the top and boot the snap.
run co de info. This will give you updated drive info (print). compare to your first one.
access the individual drives verify which one has the data.
Now copy all data from your original hd to the new one, now your data is backed up to a new drive. Swap your original HD back out (for save keeping)
You should now have the data on the bottom new hd on top.
Now copy the data from the bottom to the top drive.
You should now have duplicate drives
Now use the web interface and have the snap drive utility setup a RAID1. It will give you a warning that all data will be lost on the second drive, will not matter since you now have the data on both drives.
I have had users use dd and do a raw copy form 1 drive to the next. If you do this with a mirror drive you just resynced the drives. Every rime I use dd I write the drive designation down. Then I write out the dd cmd line I'm going to use, triple checking. Then when I type it in I triple check it again.
If I understand AD correctly. All permissions are controlled by the server. As long as you keep the share names the same and have the correct map there should be no problems.
The document posted for repairing a broken mirror was sent to me from a individual when I bought my 2200. Clamming he was a snap tech that got laid off. It only works if the drives are the same size. And I have never used it. I'm always changing capacity and it does not work.