There's no way the two WCG accounts you linked to could have the same CPID, as they are two totally separate accounts. If you mean that one of them shares a CPID with other projects and you'd like to sync the higher-credit one with those, that is possible. You'll have to align the WCG account you want to "keep" with your other projects, by using the same username, email and password that you do for BAM, and request that BAM reset your CPID on the "Main account page". Once the account information is lined up, it SHOULD even fix itself after a while. Just note that WCG does not play terribly well with BAM, so you may get some error messages here on the site but they shouldn't affect what you're trying to do since the changes you would be making will ultimately be pulled from BOINCstats, which aggregates stats from the projects themselves.
Merging two accounts would have to be done at the project end since BOINCstats is just collecting data from them, and I've not heard of any projects yet that allow this.
As a way to prevent this sort of thing from happening in the future, if you are using BAM you can change your account information once--at BAM, and it will be distributed to the other projects. WCG may need a manual change, because of the reason stated previously.