When the pool is set to floating, the user will most likely get the same desktop the next time he/she logs in. Therefore the files are lost for that user either way. You should also not make a linked clone pool that you never refresh/recompose. To solve your problem i suggest you look at the possibility of redirecting those application files to either the roaming user profile or a network drive. Another solution would be to use ThinApp on your application. That way you will be able too keep all changes the application does in a sandbox.
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