Background info on how I came upon my solution: (If it's TLDR, just skip directly to the solution further below.)
I experienced a similar issue and have been able to fix it. In my case, it is because the Companions turned me into a Werewolf from being a Vampire Lord. I had none of the Vampire's abilities and weaknesses, except Resist Disease 100% and I still have the ability to turn into a Vampire Lord. While at the same time, I also have the ability to turn into a Werewolf (Beast Form) and have the Werewolf 'Resist Disease 100%' ability (yes, I had two Resist Disease 100% abilities), making me some sort of messed-up Vampire-Werewolf hybrid. Clearly, something must have messed up when the Companions turned me into a werewolf.
Like what happened in your case, Lord Harkon and his court won't recognize me as a vampire. That is except for Serana, which recognizes me as a vampire and doesn't give me the conversation option to turn me back into a Vampire Lord. Entering the
player.setrace <player race>racevampire console command gets me recognized as a vampire by the court (Serana still won't give me the conversation option to turn me back into a Vampire Lord), but I still had none of the Vampire abilities and weaknesses I previously mentioned.
Solution (or: TLDR)
- I entered the
player.setrace <player race>racevampire console command (I'm not sure of an alternate method for the console command for non-PC players, but you could try either turning into a Vampire, vanilla-style or just continue to Falion as I will further explain below.)
- Get Falion to cure me of my Vampirism, through the Rising at Dawn quest (which also cured me of my Lycanthropy, for some weird reason).
- Go back to Serana, who now recognizes me as a non-Vampire and now gives the conversation option to turn me back into a Vampire Lord.
- After I let Serana turn me back into a Vampire Lord, I am now not a messed-up Vampire-Werewolf hybrid. I now have all the abilities and weaknesses of a Vampire and have no Werewolf abilities anymore. Damn Companions.