Thanks, Keith! I was waiting until I got some word back from this forum, I hoped, before proceeding. Your plan sounds perfect. I'll be restoring from Apple's Time Machine, which gives one the option of saving the original, which seems like the equivalent of 'copy to a different place.'
So after the backup I'll move the restored copy to a workspace and rename the original without the '.orig.' tag or whatever Time Machine does to denote it.
As for the links between transfers, I don't see a problem about those. They will still be in place in both accounts, just not linked, if I understand you. The only reason they are important is that they have to be ignored as income on one end and attended to at the other for tax purposes. But my categories are set up as the primary tool for tax info, and I usually have to tell the reporting process to ignore transfers. When QIF export time comes, I'll have to sort out whether Checkbook Pro thinks transfers between accounts are of tax interest. But that's another story…