Some thoughts... I use CDWave to do my tracking...
I save the CUE Sheets when I do it so I can easily fix any track marks, etc. I started doing this when I had a bad track in a Seed once that I wasn't able to fix it perfectly... But now, by using a CUE Sheet, I get the same exact tracks if I need to re-do it in the future...
Greenone can attest to how useful this is - he accidentally deleted something off a HDD I mailed him losing some of my 16/44 tracked WAV files, but he was able to re-create them using the Master 44k WAV and the accompanying CUE Sheet.
If you had saved a CUE Sheet, it would be easy to reload the entire set into CDWave (or whatever) giving you the same exact tracks. Remove the offending track marker and save you files...
For what you need now, you can use SHNTOOLs to "join" the two WAV files back into a single WAV file. Rename it, and all the files that follow and re-do your FFP/MD5s... That's how I do it, but there are a million ways to do this perfectly...
Terry