The use of doHandle404() should be abstracted away from you in the ACS Commons provided 404 overlay [1] which you shouldnt be changing.
You should only have a /apps/sling/servlet/errorhandler/404.jsp that includes the ACS Commons provided 404.jsp (per the instructions).
Can you check to make sure that /apps/sling/servlet/errorhandler/404.jsp is setup properly, and that the deployed file at: /apps/acs-commons/components/utilities/errorpagehandler/404.jsp matches [1].
If that is the case, then it sounds like you have a JSP compilation caching issue which can (usually) be resolved by restarting the Sling Scripting bundles.
Also - you can log a GitHub issue for future issues here: https://github.com/Adobe-Consulting-Services/acs-aem-commons/issues
HTH!
[1] https://github.com/Adobe-Consulting-Services/acs-aem-commons/blob/master/content/src/main/content/jcr_root/apps/acs-commons/components/utilities/errorpagehandler/404.jsp
[2] https://github.com/Adobe-Consulting-Services/acs-aem-commons/issues