I think the English sentence "I do not remember what I had done" is not really correct. You would rather have to say "I do not remember what I did". Past Perfect would be correct if the first part of the sentence was "I did not remember", but like this normally you don't use the past perfect (at least it's like this in German, and I think in English, too).
My Greek is not good enough, but I would say that in Greek the same rules apply, so the sentence should be either "Δε θυμάμαι τι έκανα / έχω κάνει" or "Δε θυμήθηκα τι είχα κάνει".
I hope this is correct. Maybe someone can confirm.