Be sure that if you're updating a Javascript file that you take the time to update the version of the file. SAP Portal does this using a query string like construct after the javascript file for its OOTB components.
You can do a similar construct for your files by simply embedding a version into the file name. Following the previous GA example, you can simply update the file name to be ga-split-2.0.1.js
Of course, the next step is to update the PortalComponent to pull in the correct version of the file.
So why do you need to do this? Depending upon how your Portal and Load Balancers are setup with caching and expires headers, you won't push the correct version of the javascript file to the browser unless you update the file name! Why? It's common practice to set Expires headers in the far future and set the browser to cache the javascript file. If your setup is doing that, then any changes you make the the original JS file will not be pulled in unless your users happened to clear their browser cache. Since the chance of your entire user community pulling that off is miniscule, the only way to force them to get the new version of the file is to update the file name!
Also, be sure you head over and look at what Spyvee did to inspire these posts over at NetweaverCentral.