Charlotte was Charles’ only child, and an illegitimate one at that. Bonnie Prince Charlie had never married, being so focused on his right to the British crown. Even if Charles did gain the crown, the line would have died and the crown would have passed onto the Hanoverian line after all. Of course, this may have been different had Charles not started drinking and married his mistress, making any children between them legitimate.
He did eventually marry, but it would be too late for him to have any children. There were later claims in the 1800s that Charles had a legitimate child with that wife, but there is no evidence to support this. Considering Charles signed an act of legitimacy for Charlotte, it would suggest that there were no other legitimate children.
Interestingly enough, he did offer to convert to the Protestant faith in another attempt to gain the crown. While he went through the ceremony to convert, by the time of his marriage to Princess Louise of Stolberg-Gedern, he was Catholic again.
Charles died in Rome in 1788 and was initially buried in the Cathedralof Frascati, where his brother was the bishop. When his brother, Henry Benedict Stuart, died, Charles’ body was moved to Saint Peter’s Basilica, where his brother was also buried. This was also the burial place of his parents, so the family could be together. However, his heart was left at his original resting place.