Ideally you should just get used to the channels being out of order

Of course that is not for everyone, so the crude hack I have used to prevent this issue is to set the headend ServerVersion value much higher than the current value (eg set to 500). When a lineup change occurs then your existing channels have a higher version number and are left alone.

The problem is that this hack cannot be undone easily, so if the emulator is majorly restructured and the station serverids get changed (unlikely), then your tivo will no longer receive data for the changed stations and may need a "clear and delete all" to get rid of the hack