Modifying an Existing Entity Column in hook_update_N
cache_clear_all() with no arguments clears cache_block and cache_page only; entity and schema cache both live in the cache table, so clearing that bin explicitly should do the trick:

cache_clear_all(NULL, 'cache');


Or if you want to clear the specific entries:

cache_clear_all('entity_info', 'cache', TRUE);
cache_clear_all('entity_property_info', 'cache', TRUE);
cache_clear_all('schema', 'cache', TRUE);


I'm assuming you've already updated your hook_schema() implementation to match the new scheme, or implemented hook_schema_alter() for the same if you're doing this on behalf of a different module.