One of the EPG experts (someone like Impact) will give you the specifics on how it works, but I think what happens when you rerun the guide setup (& rescan), the channels you end up with have deep down different technical identities to the previous versions, so even though the channel that the scheduled recording is meant to use is there, the guide or scheduling engine doesn't see it as the same channel.
The easiest way around it is to change the series settings to record from any channel, but then that means you might get the SD version instead of the HD version.
Doing series recordings via keyword will work too, but again you might get SD instead of HD.
I think that exporting & re-importing recording.xml will result in the same problems.
I don't know a way around it.
Justin