Resolution:
Typically, when there are multiple versions of a particular transaction, the version that is used most often is configured in the Protocol Editor. For the other versions , the operation is specifically bound to the Trading Partner which uses them and the particular version guideline file is used to override the one that is configured in the Protocol Editor using the "Binding Modifiers" feature.
This is the recommended practice.

For more details read the section on  "Binding Modifiers" in BC EDI Protocol Guide.