hybrid8,
Mp3/Tag Studio supports extended track numbers in the current version. Only early versions did not support this.

Also, there's an undo-feature in Mp3/Tag Studio that can fully restore your files to the original state whenever the result is not fully satisfactory (although it's probably too late for that in your particular case now ). There is also a preview function, so that you can verify that the results of any operation are what you like, even before touching any single file.