Ahh the woes of attempting to load on updates of your Android version with a rooted phone. Often times, completing this process breaks your root access, resulting in you having to go and acquire the root capability back, although this is not always an easy process and can sometimes take longer than expected. A recent leaked build of Android 4.4 found its way onto the web for Galaxy S4 owners, and sure enough, it made root access difficult for many by breaking SuperSU. This is the part where most of us might piss and moan about it happening, only before finally attempting to search for a solution to our problem. Thankfully, with this particular case and the Galaxy S4, Chainfire, a popular and must have app for root users already has the problem fixed for you.
If you point your browser over to the Chainfire website, located here, you'll be greeted with a new flashable zip file (version number 1.89) that will help you get your root access back and fix the issue with SuperSU. It's also worth mentioning for those of you that use CF-Auto-Root, that it has been updated as well to contain the new version of SuperSU 1.89 and you can download that here, so you don't have to download the new SuperSU version file directly. Chainfire mentions that this new CF-Auto-Root has been tested with success on the leaked Android 4.4 based ROM on the GT-i9505 (which is the Galaxy S4), but that it should also work with other devices as well if you need or want to add root to those.
On Chainfire's G+ post, he also mentions that you can find useful information about this topic in the official XDA thread, and that while Google Play Store download access will show up at some point, at the time there is only one leaked ROM available for Samsung 4.4 compatibility, and adding Play Store access for the download could break root for some users as this update triggers a binary update, which almost always results in some users losing root. He further goes on to state that as more ROMs become available, he'll more than likely move onto publishing the Chainfire app update to the Play Store. If you or someone you know owns a Galaxy S4 and has lost root access, and SuperSU has broken for you because you loaded on this leaked ROM build of 4.4, this is your solution. A hefty thanks to Chainfire for his hard work and dedication to fixing this problem.