Going by your picture, you're still feeding both cameras in to the codec, and still providing the Ethernet control of them, so they should all still work fine. The only way this won't work properly is if you swap the two cameras over with your matrix switch, then you would then need to control "camera 2" to move the one that is now showing as "camera 1" and vice versa.
If you just want to swap the cameras over, you would be better using the xAPI to swap the camera inputs, Or, if you're wanting to do some layouts, you may be better off controlling which camera is seen where on the screen using the in-built Video Compositing functions that are available the newer releases of software (since CE9.5).
Wayne
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