It depends on a few things.  Is it safe to assume you have created your port channels over multiple modules?  So each member of the port channel is on a different line card?  That is what is recommended so that in case a line card fails you are still up and running.

I would install the gen3 module on both chassis, assuming you have slots available, and add a link into the port channels from this module.  So today if you have in the chassis a 3 link port channel that looks like this:

slot 1 port 1

slot 2 port 1

slot 3 port 1

I would add slot 4 (gen 3) port 1.  Then I would remove the members from line card 3, and then safely remove the line card.  I am assuming you have your port channel spread out over line cards.

If for example you had a port channel with 3 members, and all 3 members terminated on a single line card, you could do the same as I describe.  You just have to increase the size of the port channel by adding additional links, and then removing the legacy links, and thus the line cards.

Things to keep in mind are that you have to make sure your speeds and attributes match. So you can add the member in with the "force" command, to make sure you are ok.  For example, perhaps your links today are only 2GB, in that case your gen3 members can only be 2GB.  Once you have the gen2 card removed, and no links exist in the PC from the gen2 card, you can increase the speeds all at once.  I fear this may be disruptive but it will be very quick.

Brian