With the current functionality available in MC you should be able to import an XMLTV file for the channels that have no data, in addition to your normal EPG data load.
You would need to create the dummy XMLTV files externally to MC, and it would need to have the correct dates and times for the period concerned. But that is all doable.
The other alternative is to find an XMLTV EPG source for the channels that currently don't have data, and load that using MC functionality.
I believe there is good reason for not having channels with no EPG data show up in the Guide. Something to do with Grouped and/or Stacked channels I think. A search may find some reference to it.