It could be a good occasion to
go for the SEO premod, since you'd be updating almost all SEO mods.
If your phpBB is up to date, then it will be very easy to merge with for example winmerge because the only differences will come from the phpBB SEO mods, always identified by comments in php files.
Other wise, and since there are many versions since 0.4.6, I assume that un-installing 0.4.6 priori to install the latest version would be the fastest. You would just need to keep all files in phpbb_seo/cache/ and make sure you keep all the custome settings (static parts, delimiters you could have set in phpbb_seo_class.php and put them in phpbb_seo/includes/setup_phpbb_seo.php where they now are set).
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