You can tell shntool to fix the entire set and it will fix just the last track. I don't think you need to use the -noskip option but try it if the regular way doesn't work. But if you know it's just the last track I personally prefer the -pad argument as suggested by RainDawg

Q: Why are you concerned with fixing this last track? My view is that if all you are doing is archiving or burning files that you got from someone else just leave the last track as it is. An SBE on the very last track doesn't matter. BUT if you made these files yourself from wav files then it's good practice to get rid of that SBE even on the last track before you spread it around. It saves newbs like yourself the trouble of wondering what to do about it later.