@MoiraGoggin - not entirely without warning - the warning that comes up indicates that you will no longer be able to process cards in this company code. (I don't have the exact message handy this morning). Reading that message does not exactly explain that the GUIDs for the credit cards are going to be moved from the vault.
Hind Sight is 20/20 of course and after thinking it through, it makes perfect sense that this is what would happen. The newly copied install is pointing to the same cloud vault that you live installation is using. As soon as I hit the OK button on that message, the next message was ""transferring credit cards from vault"" which was a little better description of what was happening. but it was a little late at that point.
Sage Payment Solutions can correct the vault but it was not a quick fix.