Playing as Daenerys, and having conquered Westeros, I find that I have the decision to 'Legitimize my Targaryen Heritage'. The tooltip for this decision says something about declaring yourself the son of Rhaegar, so I assume it isn't meant to be available to Daenerys, but is instead meant for my husband, Aegon. However, at this point, Aegon is already shown as being Rhaegar's son. Taking the decision doesn't remove it, and also seems to kill a few random Valyrian courtiers every time.