If you have dispatcher configured in your enviroment, delete the content of the cache directory in the dispatcher, the docroot directory.
Hope this works for you.
Miguel Angel Sánchez-Guerra
I believe your question is regarding the publish instance and not the dispatcher.
If so then there is a known issue with CQ5.4 regarding jsps not compiling during activation. To force recompilation of jsps you would have to delete the cached compiled jsps under "/var/classes/org/apache/jsp/apps" and restart the jsp script bundle (Apache Sling Scripting JSP Support - org.apache.sling.scripting.jsp) in felix "bundles" console.
The above step should clean out the "old" jsp cache and on next request to a page/resource these jsps should get recompiled with the latest changes. Also contact daycare for a HF for this issue.
If however you are facing issue at the webserver level then what Miguel has stated above should help.