If you consolidate Microsoft Windows 2000 Forests that have different extended Schemas, then you will only be able to keep one of the extended Schemas. This is a Microsoft Windows 2000 limitation. You must decide which Forest will remain and use Microsoft-provided, or third-party [NetIQ Domain Migration Administrator (DMA 6.x)] migration tools to migrate objects from the "foreign" (the Schema that you will not keep) Forest to the Forest on which you will maintain the Schema.
You would treat the "foreign" Forest as if it were a downlevel NT4 domain to be migrated to a Windows 2000 domain. All Schema changes made in the "foreign" Forest will not be carried over as you migrate objects to your chosen Enterprise Forest.