It might happen that a port will go "error disabled". This will take a little while before happening (I'm not sure if it's 1 hour or 2 or maybe even half an hour), but when a port gets in this state, you'll need to "shut" and "no shut" the ports on both sides to get the ISL's up and running again. The portchannel wil restore itself after that.
AranH - Good question about the redundant fabrics and ISL. The two fabrics were implemented by EMC with an ISL. The first switch is vsan100 and the second is vsan200 and the isl (2 ports on each switch) is vsan 300.
I'm not sure why EMC implemented it this way. Every host and every storage port has it's redundant counter part in the other switch/vsan. I'm not sure why we would need an ISL for this. Maybe it has something to do with Fabric Manager being able to see both fabrics at the same time.
Brad, I am not sure either why they would have implemented two switches with an ISL without a specific solution that required it. Ideally you would have each fabric logically and physically separate to prevent any fabric wide problems from affecting your entire infrastructure. You have physical redundancy with your current setup, but with the ISL there are shared logical components.
If you have the FM license you can manage both fabrics at the same time. Other wise you have to open one at a time. Not sure how the ISL affects this, but IMHO it is not a good reason to connect your fabrics.
I would assume the ISL was created for the ability to grown as the SAN matures. You can always just block the ISL connection between the switches. What usually happens if you isolate the switches though is that you have one resource on one switch you need on the other switch. You can always recable but having an active ISL you can use is faster.
Back in 2.x and early 3.x you weren't required to have a license installed to see multiple fabrics at the same time. You were technically suppose to have the licenses to be not in violation but Cisco didn't enforce it. Cisco decided to close that backdoor around the license. Cisco is closing down even more licensing back doors in 4.1(1) so if you like the features of FMS, you'll need to ensure you are correctly licensed going forward. In 4.1(1) you can't collect PM data on switches that don't have FMS licenses. Each and every switch will need to have the license or you won't be able to pull stats or run reports.