I think you're doin it backwards
Here's my understanding:
1. All updates are through the PFD now, only, but with both PFD and MFD powered on. The sync will begin after the system reboots and will take a few minutes (hence, monitor MFD Aux page before powering off, else you'll get a Sync Error)
2. The Standby DB is only for newer (ie not-yet-valid) data, not older. The Active is for current or "most recent" data.
So loading the previous cycle into the Standby probably borked those assumptions above. As you say, the next cycle will probably flush everything out if you load it into Standby. If the error message annoys you, you might try loading the current nav revision into Standby also, but it might not allow you if it detects that your navdata is no better than what's already in Active.
What a pain, eh? I guess once the flow is sorted, it's easy, but I didn't even know to expect this new way of things...