Is this going to be like the BBC2 swap and mean we have to modify all series links on those channels?
No channel IDs will change on the network, so your series link will just migrate with the EPG number change. There are only issues with series links when channel IDs change. eg. The new scottish STV HD regions were introduced.
As a Very Insightful Person, I'm here to share my knowledge. I don't work for Virgin Media.