mod_deflate should look for the Accept-Encoding header and compress if acceptable based on how your output filters are configured.
My CMS compresses all htm and js files on my own computer and uploads to the server the compressed files.
are these compressed files uploaded as .gz file types? are you also uploading the uncompressed versions?
you should only use "AddEncoding gzip" for the gzipped versions of the files and you need a way to serve uncompressed versions. i don't really see a clean way to reinflate/decompress the output of a precompressed resource based on the Accept-Encoding header.