Suggested Solution from Customer Service:
I found in Main Settings-Product Identifiers that we can set an extended property for the barcode to be used.
This is still suboptimal for us when the barcode is filled with a non-UPC/EAN number, requiring an additional "Does not apply" value in an extended property.
I suppose we could run query, import and export, but it is extra work and more chance for error.
When you have both UPC and/or EAN barcodes in use, it is best to place that barcode(UPC when available, EAN if not) in the Barcode field in General Tab and not in Product Identifiers Tab, as you cannot specify two or more extended properties for barcodes in configurator Main Settings-Product Identifiers(e.g. ProductIdentifier.EAN, ProductIdentifier.UPC, ProductIdentifier.Custom ID). The configurator matches the type of barcode in the Barcode field correctly when listing to eBay when you leave this option blank.
So is anyone else facing this challenge and how did you solve it? Any advise would be greatly appreciated before I embark on this.