If Haggar went by the name Honvera before the war, is it possible Lotor went by Sincline? If so, then it's possible Allura does know Lotor, but knew him as Sincline and just doesn't think they're the same person. Also she and Coran don't share information about the past unless it's immediately pressing, they didn't tell anyone about Zarkon, Haggar, or the original paladins until they had to. It's possible they wouldn't say anything about 'Sincline' if they thought he was dead and didn't matter.
I’ve considered the possibility Lotor wasn’t using the same name in the past.