The behavior you described is not the intended one. Let us make sure we understand how you did it.
Is this (see attached image) the window you are talking about?
If so, you notice that there is an "Auto Match" button. You do not need to click the button unless you found many empty entries in the list. You may notice that in my screenshot I have a lot of unmatched entries (those with the words "(click here to configure)"). That is because those channels are cable channels, and I was only running the tool for my over-the-air ATSC channels. So that was OK.
Regardless whether you clicked "Auto Match" button, if you found some channels that are mapped to wrong ID, i.e. your channel 5.3 gets mapped to 5.1 data, you can click the entry and get a drop-down lost of entries. The top of the list is an empty entry. Choose that to clear the wrong data.
Once the mappings are saved, the next time you run Load Program Guide, the same mapping (including empty mapping) should be used, unless you click Auto Match again.