The issue was caused because if you link the chassis cmcs via the internal switches, updating the firmware on the switches causes the cmc to power cycle the chassis and corrupt the update. (tbh this is a pitfall that shouldn't exist)Avoid this by connecting the cmcs directly or via an external switch during firmware updates.The firmware on the switches is corrupt, I think it should be possible to reflash the chips directly however this would require electronics expertise.  In our case the seller replaced the switches under warranty and we were able to update those successfully.
On updating IOM firmware 2 out of 4 m6348 failed to update and now report fabric mismatch.  I have tried the update process again and reseating them.  They won't even power on in the enclosure to access the console, is there any way to recover them?
IOM firmware on m6348 switch failed, fabric mismatch