Propagation Tool - loses CM links

Hi,
We have a WLS 9.2 Portal. We have deployed to System Test and propagated in all the Visitor Entiltlments and Content Management (Content + Types) that our application requires. Only problem is, that if we deploy a new version of the application EAR, all the CM links are lost. So where once before a user logged in and they saw a personalised image, after the new EAR deloyment they don't. The image is still in the CM, and can be viewed through the Portal Admin console. If before the deployemnt we take a backup 'propagation' and reapply it after the deployment the CM 'links' are back and the images can be seen again.
I assume this is a basic problem, and there is something trivial i'm doing wrong. Or are you supposed to take a back up everytime before your deloy a new version of the EAR.
Thanks in advance,
Anthony

Russell,
Appreciate the answers. No problems in following the steps of a propagation export from source, deploy the EAR, propagate the new propagation structure. This will cater for moving from environment to a new environment.
Where i would have a problem is where the destination has content that it wants to keep. When we do a merge, some of these CM 'links' get lost. So advice on this would be great. We only use the Propagation utility in Workshop to propagate, so we can see exactly what we want to propagate. We don't use ant scripts. And this scenario is the one that needs to be catered for as this is for production fixes, releases when the system goes to production.
When i say CM 'links' i mean that whatever framework weblogic has set up under the hood for the content to get displayed. All the placeholders / content selectors are there, and there are no errors thrown, but however that framework hangs together, after a deployment they don't work, and after a merge propagation they don't work.
Thanks for your help,
Anthony

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