However, although we had redundant paths we still lost all communications with the NetApp!
Basically if you change the flowcontrol of the switch port to ON, this may be incompatible with the Flowcontrol of the Etherchannel. It is not possible to set the flowcontrol of the Etherchannel in the Web Interface, it is only possible to set this in the CLI.
The effect of this incompatibility is that the entire etherchannel is suspended and communications are lost to the Filer.
Be aware if you need to make these changes SHUT DOWN ANY SERVICES THAT ARE USING THE FILER FIRST.