I think I'd search the source for md5( and check everywhere to see if it's a place that needs to be changed. Actually I think there may only be one place where it does a hash on passwords to compare them to the database (but don't hold me to that).
I wouldn't tell you not to do it, but I do wonder why you want to because if you have a password a user enters you can check it in either database by applying the right functions, and there doesn't seem to be any reason to store the same encrypted value in two databases.
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