My own cursory knowledge of law probably does not apply, but it does not sound like you made a profit by re-selling the application with your changes, so you should be safe from lawsuits by SCO. When you found that the application could invalidate your data, did you go to the software company and ask for a fix? If they refused, then you may be able to sue them (if you have in writing that the application promises to do so-and-such). Since they are bringing the suit, they have to prove that your changes have somehow damaged them.

In general, I do not allow any schema (or data) updates to a third party application database, as this can invalidate the service contract. Extra lawsuits have never come into the picture (as far as I know).