I think it's safe to say he does NOT remember
Mewtwo anymore, and that all possible records were destroyed. Keep in mind, Giovanni is a villain in a children's cartoon, he's not going to think that far ahead OR factor in a possibility that he might lose against the protagonist. This isn't Criminal Minds where the bad guy is always 3 steps ahead until the very end. His goals are very straightforward and his plans to meet those goals are always full of holes.
The
Mewtwo plot has run its course. What do the writers do when a plot has run its course? They throw in some bullcrap Deux ex Machina to ensure that the plot is finished once and for all. They've done this several times. Remember Soledad and, perhaps the most infamous example of this, Tobias?
Yes, Giovanni MAY have anticipated the destruction of New Island, but the scientist in charge was neither Professor Namba NOR Dr. Seiger, so any records he might have had left would have most likely remained with him, and when Mewtwo erased his memories, those records could have been removed from him, because it is a children's cartoon and the writers got tired of that plot.
All of that being said, I would LOVE for Mewtwo to come back into the anime again, if only for a little while. but only if they can get Dan Green to voice him again, but I don't think Sexy Amnesiac Pharaoh would have time to because of his personal issues. :( But I digress.
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