Hi,
As there is no easy and recommended way to achieve a live xm->xl instance migration right now, you have to reboot all the nodes and all the instances eventually.
My suggestion is to:
1. Change the xen_cmd which Ganeti uses to xl, making Ganeti pretty useless because it will not be able to issue any more instance-affecting or -inspecting commands.
2. Change the toolstack on a node, reboot it, make sure the instances are back up through xl list.
3. Do the same with the other node.
4. Check if all is well with gnt-instance list and gnt-cluster verify.
You will not be able to migrate instances between the xm and xl stacks to ensure they remain online, so make sure to plan for at least some instance downtime.
Cheers,
Riba