It has been quite a while since I have used NT4, (that is where the BDC and PDC roles were established), but I do believe you have to promote the BDC to the PDC before it will take over the duties.
If you are not using NT4 then you are just relating the names incorrectly. After NT4 there was no such thing as a PDC and BDC. All domain controllers were just called DC’s since they were equal except for the Global Catalog server which is the first server that you installed on the network. It would take over all FSMO roles, (Flexible Single Master Operations server). Can you bring the main server back up? If so go ahead and bring it back up, then promote your second server to also be a Global Catalog Server. Then assign all FSMO roles to that server. You should then be good to take the other server down. Let us know if this is the situation and if it worked.
Here is some info on the FSMO roles: Managing Active Directory FSMO Roles.