If editioning or numbering, the right thing to do would be to act as though the previous signed prints were appropriately labeled. Thus you might, as you thought, start with #3 if you had already done two of that same print size.
If the prints were not signed, though, that is a different issue. I would argue that unsigned prints are not, by definition, endorsed by the artist and so would not count towards any edition or numbering. Others, I am sure, will disagree. Both sides will have valid points.
It's important to remember that very few editions ever really sell out, so erring on the side of caution and including the previously made prints will probably not effect your pocket book.