In the books Harry has had some gaps in his memory, and other things that suggest he may have had his mind messed with. Eb as the Blackstaff does have the authority to mess with Harry's mind if he deems it necessary. This could be a pretty big deal from a story perspective if Harry finds out that his grandfather has messed with his mind, so it would make some sense.
If I had to guess it would be memories removed, blocked or altered. He'd have done it to protect Harry, or because he thought he was doing the right thing (sounds a lot like Harry). If so I think Eb would restore them when he's about to die.