If you mean that you plan to rip an audio CD that was burned with SBEs then you can only fix those SBEs with a wave editor.

You have to zoom in to the last sector of each track that you suspect has an SBE and look to see whether there is a sudden drop to silence there. If so, you have to snip the silence off.

Now apparently this could be done at the ripping stage by telling EAC to 'remove digital silence' or something like that. I've never actually done this so I can't say for sure that it would work. But it wouldn't hurt to experiment.

Once you have the wave files fixed and the SBEs removed, you then would run shntool over each musical set in order to realign the tracks along sector boundaries. Or you can compress each musical set to FLAC using FLAC Frontend and set the program to align along sector boundaries.

I hope this helps get you started.