Presumably by falling back to the lowest version supported by both sides, with negotiation done in 1.0 encoding or so. It's a standard technique. Also note that

Presumably by falling back to the lowest version supported by both sides, with negotiation done in 1.0 encoding or so. It's a standard technique. Also note that PCIe is point-to-point so no downgrading for devices just idling on the same bus.