(Call Mewtwo up again and have him testify on why he wiped their memories? Ash can corroborate that statement straight away with the events that led to the memory wipe. As can Meowth, James, and Domino. She also offered to get her therapist on speaker phone to explain the exact nature of memory-wiping.
As the wiping was done in self-defense (and to prevent harm from a protected landmark), that could work for Phoenix. Luna Carson's memory was wiped, too, but she does have a lot of information on Mount Quena itself and can attest to its protected status. She's written papers which are available with just a quick search, and those would contain pertinent information on Mount Quena. Also, the Johto Historical Society and Land Conservancy would have information that's public record.
In regards to the memory-wiping, Giovanni, Domino, and their troops were transported unharmed to a local airfield, where they left on their own accord. Giovanni's memory wasn't fully erased, but repressed, as he did have a feeling that something happened, but he couldn't quite recall what. When questioned about his sudden arrival at the airfield, he can mention the missing time, which would corroborate the incident, as Domino can testify to how long the operation took place, along with provide records.)