How to recover deregistered AMI and keep ID?

I had deregistered some AMIs in a region I believed was not being used anywhere in the current account, and indeed AWS gave me no warning that the AMI IDs were referred to anywhere.

Unfortunately I didn't realize they'd actually been shared into another AWS User Id/account where they were being used. I found out the hard way when the auto-scaler failed to start a new instance.

I've worked out how to restore them from another region, but now the AMI IDs are different, which would presumably mean I need to update CloudFormation scripts etc. to use the new IDs.

One of the machines using one of those AMI IDs holds persistent data on it, and I certainly don't want it replaced the next time the CloudFormation stack is updated.

What can I do to tell CloudFormation to leave that server alone - termination protection? But will it allow the rest of the stack to be updated? Is there anyway at all of recovering an AMI so it has the same ID as it did before?

I will say the whole concept of AMIs being shared between what I thought were entirely separate AWS accounts threw me completely. What's the best way of copying an AMI from one account to another so that is not "shared"? I can't see a way to download/upload a snapshot from the console.