Do you mean the "IR Blasting details" rather than the "tuningdetails"
Apologies if this is a stupid suggestion, but can't you re-number your channels.
This won't work once they have been combined, but if you clear all the channels, and then scan both set top boxes, you can then edit the channels numbers for each one before combining. If you ensure that the channels numbers of the channels you want to combine are the same, then would this fix your problem?