i am backing up some of the games i have, protected with different method (safedisk, etc). I made the CD images with alcohol and made BIN/CUE file.

The CD's has some empty space (doesn't fill 700MB), so if i add to those images some extra files (the updates of the game) using some program (WinISO, UltraISO, etc), will the output BIN file still have sub-channel data, or will it be messed up?

More than likely messed up.

If you have a CDRW handy give it a go and see what happens. Most people learn by doing. I do at least.

I would also think that the protection would do a sector check and the different sector numbers would screw it up.

Almost 110% sure your CD would not run the game anymore.

Both safedisc and securom, and probably others check for the length of the CD : if you add data at the end of it, your CD won't run anymore.

The only thing you can do is to modify individual sectors with an hex editor, and you can add, with lots of patience, at most one or two small files where there would normally be the post-gap (blank sectors at the end of the image).

Anyway after that you need to edit the TOC to add the references to these new files (hard - but you can't use ISO editors as they would rebuild the whole file structure), as well as rebuild the ECC/EDC fields of the modified sectors.

I have tried something like this, adding a patch to a protected cd after burning, and it refused to run anymore.