After disabling mapping relationships for loading, you should validate the schema with those schema objects removed to ensure that the changes will not result in validation error during loading.
Save the changes to the CMF file before running the validation.
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Click Tools > Schema > Validate Schema for Loading.
As part of this validation process, all objects marked as disabled are removed from
the schema, as well as all relationships for those objects or interface definitions
that were marked as disabled, are removed from the schema. Once the validation is
complete, the removed objects are returned to the schema.