VDP is now a dead product so I don't know if there is going to be any joy in this. My advice: choose a backup application that has a future.
While you are correct that VDP is on the way out, vMware is still supporting the product and released an update last month. You would think something like certificates that have been expired in excess of a year would have been included in that update or previous updates for that matter. I will not be leveraging VDP forever but in the interim this is still a problem that needs to be addressed. There should be a mechanism to update the certificate either way, I just assumed others must have encountered this issue and had a way to resolve it.
I assume you ran the regenerate command when you were "root" and not "admin"
I don't think admin will let you update the keystore