How can we clean up app bits WAS server leaves behind upon EAR file deployment

We are running WebSphere v5 in a Windows 2000 environment. When we do a deployment of our application EAR file (remotely from our workstation to the server and through admin console), the WAS server seems to leave bits of the old application in a sort of "cache." This does not allow our new deployment to fully deploy the latest changes. How do we clean these up (where do we even find them?), and what do we need to do in our future deployments to remedy this situation? Thanks in advance for the help.
I have personally not encountered this particular issue, but it seems to be a serious product issue that I would expect IBM to be aware of. My suggestion is that you contact IBM support to understand whether or not this is a known issue and when it is likely to be resolved (in which release). They should also be able to suggest possible work-around. If you do not have a support contract with IBM, you can get Developer support from IBM developerWorks at no cost.

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