This issue can be resolved by reloading the VDX6940.
A similar condition can occur between two VDX6740s. The link will be up at both ends, but recognized as ISL on only one VDX6740. The VDX6740 that recognizes the link as an ISL may also be experience MAC learning issues per the following article. MAC Address table not updating correctly on VDX fabric
The same condition that causes MAC learning problems described in that article can also cause a VDX6740 to fail to send the signals that the link partner needs to recognize the link as an ISL.
Regardless of the specific model of VDX, if a link between two VDXs is recognized as an ISL at one end and not the other, the VDX that is able to recognize the link as an ISL should be reloaded.