Of course, any modifications made to the ear at runtime will be lost when the patch is applied, since the old version of the module will no longer take precedence on the module path and will not be used.
I recommend you talk to the portal folks about how I recommended they deal with a requirement to use an exploded deployment. In their case it was user-modifiable and couldn't be deployed from inside a module.
Better yet, just write to the data/ dir or something and don't write inside the ear.