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Hmmm. Well, if your in NATIVE mode, you can't use anything from the NT 4 Domain as NT 4 Domain Controllers are not allowed in a Native mode 2000 AD.
If you have a trust relationship setup you can treat it as another resource just like when in NT 4.0
Not sure what you mean by Migration though. If your users are in AD, then they don't have same SID history as they did on NT. You might be able to "MAP" the old NT SIDs to the NEW AD SIDS, but then I'm not sure if you could do much with that data or not.
I'm not saying that something can't be done, but sounds like a complex issue that would possibly require some dedicated effort to figure out a resolution.
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