How to resolve fatal error 'Cannot redeclare commerce_kickstart_preprocess_html'?
Because the two file paths are the same file, it suggests a possible problem with your op-code caching.

Check if you have any PHP op-code cache enabled; you should only have one op-code cache utility and may need to disable one.

You may also need to tweak your APC settings (if enabled).

apc.include_once_override = 0


Check also https://stackoverflow.com/questions/4575341/php-with-apc-fatal-errors-cannot-redeclare-class.