So when you prune posts does it simply give you a parse error or database error in functions.php, or does it execute but the post counts are reduced? I would just undo whatever changes the store hack did to the functions.php section where it might affect posts count, then reinstall that other hack in the section of function.php--
then try maybe to integrate the store hack back into functions.php with the other one.
Sorry if this sounds complex, it would require some hacking, but I can't go much farther since I've never dealt with the store hack and don't know the code changes.