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What is the difference between the File number and Invoice number?

All shipments have a File number for reference to the Customs shipment.
There is only one File for one shipment. That File number will have an Invoice number which will always show the File number for that shipment. Although there is only one File number per shipment there can be numerous A & A Billing Invoices related to the shipment.

in Customs Documentation

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NOTE: All details pertaining to CARM R2 processes are based on the current information available at the time of writing. As this is subject to change, it’s recommended you periodically check in with the CBSA or your customs broker.