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I have not read all the HH books, does he die during the Heresy? Or is he still kicking around the Palace even in 40K?

I have not read anything implying he dies, but there is no mention of him in 40K either.

To be fair is there much mention of the Custodes in general in 40k at all? Let alone specifics like names.

Do the Custodes go with the Emperor onto the Vengeful Spirit at the Siege? He could die there but I guess we won't know for like another 10 years til BL write it.

No indication that he has died but I doubt, and hope, that he isn't still alive in 40k.

I think it's quite likely that some Custodes leave for the Vengeful Spirit with the Emperor and Valdor is probably a likely candidate. But no one survives in the Emperors group bar the Emperor. Maybe he gets split off with Dorn?

Like Geek says, we'll have to wait and see.

His fate is unknown, I suspect that as with most custodes, they will close themselves off with the Emporer's "remains", their fates never really known due to their seclusion.