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I don't know if we ever resolved whether or not alt-FE would have the Falchion sword. But I do know that alt-FE has the Doctor's special Dalek-destroying baseball bat, as well as his sonic screwdriver, psychic paper, and maybe a few other odds and ends -- which all would've been looted from the dead Doctor's body in the alternate timeline (I mean, you can't let such valuable weapons go to waste in a crisis like this ¯\_(ツ)_/¯). Given that, I think it's fairly obvious how the main timeline Doctor might jump to certain conclusions. XDEh, it's no problem :P. On that topic though, do both versions of Fire Emblem use the same Falchion sword? Because from what little I know of the Fire Emblem series, the Falchion is a blade that can only be used by those of Royal blood and is supposed to be unique - something that is actually a plot point in Awakening. Given this, the sword would be an obvious hint at his true identity.
You'd have to ask @Minerva about the Falchion sword, though.