The lineup is wrong from Schedules Direct, so you should
report a lineup problem with them to have it corrected. In this way you correct it for everyone who uses this lineup, not just yourself.
In addition to this, if you don't want to wait for them to correct it, you may also be able to correct your local lineup by using the EPG123 client tool.
If Comedy Central (CC) is in the lineup at some other place, you can right click on channel 46 and select "Unsubscribe". Click on channel 46 in the left panel to select it and then find CC in the right panel and right click on it and select "Subscribe".
This should associate CC with channel 46.
If CC is NOT in the existing lineup, then it is a little more complicated, as you have to find another lineup in your area that DOES have CC in it (even if it is for another service provider), add it as one of your lineups, then do the same as above, select channel 46 in left panel, and then right click on CC in the right panel (with the new lineup being displayed), and select "Subscribe".
Then when they finally do fix your original lineup, "Unsubscribe" the channel that links to the new lineup, remove the new lineup, then "Subscribe" the channel using the correct lineup.
If you don't need CC right away, and CC does not already exist in the lineup at a different channel position in your current lineup, I would just wait until Schedules Direct fixes the problem so you don't have to go through adding the additional lineup and then removing it later. Of course, if you feel comfortable with doing this or you need CC right away, then go ahead...
EDIT: Also, updating EPG123 should have had nothing to do with this issue, this problem surely existed with the old version of EPG123. I'm guessing this means you don't record or watch much CC, so it will probably not be that big a deal to just wait for Schedules Direct to correct the lineup rather than doing manual remapping.
EDIT2: Looks like there were issues with Cox lineups in other areas as well:
https://www.thegreenbutton.tv/forums/vi ... 99&t=13841
It was also completely missing Comedy Central. They fixed it by adding the non-digital lineup for their provider and doing the mapping I mentioned above.