I've just installed v0.5.2 to replace v0.5.0 and took care to make sure my customised config.xml and epub.css files were in the plugins preferences directory.
I thought I understood from your red print notice in the first post that the updated plugin would copy the customised files from preferences into the plugins directory.
Quote:
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If you've previously used this plugin and customized config.xml and/or epub.css make sure to create a backup of the plugin folder and also copy these files to the plugin preferences folder. (The latest version of the plugin will always copy these files from the plugin preferences folder to the plugin folder.)
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Neither on linux nor windows has the 0.5.2 plugin copied the preferences versions to the plugin folder.
Edit: my mistake
I just ran a trial import, and the plugin copied the files as promised. I hadn't understood that the copy would occur on first use rather than on installation.