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I plan to use the barcode as an identifier for internal use (our products are bespoke so don't have 'real' barcodes). Would this have a negative impact with google/merchant center?
I have tried adding the identifier as a product tag and MPN via custom metafield but it doesn't work for my use case. SKU is already in use.
Yes, you may get suspended.
You can only use valid GS1 barcodes. If you don't have valid barcodes, do not submit gtin, mpn, and brand values, and set identifier exists to no.
You can also follow the guide in this video:
ok thanks