Theoretically changing the machine names should not cause the re-install of channels.......
Policy works on machine/user names and not based on GUID in AD. When policy service updates the endpoint would send up the machine name/ current logged on user name to the plugin which would in turn create a policy plan (config.xml) based on the memberships or the machine/user name in AD. This plan is then sent over to the endpoint which would check to see if the channels exist and if it is in the state (installed,install-persist etc.,) mentioned in the policy plan. If not it would attempt to put the channel in the state (defined in the plan) and if required it would re-subscribe the channel.
Are the renamed machines in the same AD group? Please send us the policy service channel history log (ensure that the log roll policy is set to daily) along with the config.xml from a target before it was renamed and after it was renamed.