The best way to transition is to only upgrade the initial PDC, and to then build all the other servers fresh and promote them into the dc status. Solves lots of issues with garbage retained on the old system that may have been NT 3.51 promoted to NT4.0, etc.
Try this, take the last BDC off line, promote it to PDC, then upgrade. Once upgraded, demote it to stand alone server (deletes the user database!) and add it to the domain, then dcpromo back to DC in the new domain. NT did not allow you to convert a BDC or PDC to simple server, but Win2k will. I would only try this if there are a lot of application you do not want to re-install on the server, otherwise I highly recommend a wipe and fresh build, as your configuration is questionable, at best.
HTH
David