I'm not sure I understand what you mean by the 5.5 and 2000 public folders 
being in different orgs, but you're migrating a user:

but you don't need to be in native mode to mail enable public folders.  Just 
make sure that if the public folder is homed on e2k, then give the anonymous 
account "contributor" permissions, otherwise the public folder won't receive 
mail.

Not sure if this clears it up.
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