GetMyAffiliates module include an option in the Configuration tab called 'Should the new partner code received replace the actual partner code for an affiliate?'
You need to use this option when:
In this case, does the code received (WEBSITE-B) replace the WEBSITE-A code?
> yes: tick the option
> no: leave the option unticked
For more information on GetMyAffiliates module, please refer to our Users Guide.