In order to update your application source, common sense would tell you to go to the application and redistribute the content (Software Library > Application Mgmt > Applications > double click your app > content locations > redistribute)
As many users have found (search technet and other various tech forums) this does not work as expected. In my case, my application installed from a .cmd. I updated some verbiage in this .cmd, primarily the .exe it was calling. No matter how many times I redistributed this and watched it complete ‘successfully’, when I went to my clients and re-ran Application Deployment Eval Cycle, it would keep pulling in the old version of this file. I even tried to REMOVE the content and then distribute it again and that also did not work.
An easy way to see what SCCM is pulling in on the client side, go to c:\windows\ccmcache and find the folder that contains your app content. I was able to verify that it was pulling in the old version by the date of the file (and you can check the contents of the .cmd)
To successfully update the content in the Content Library, do this:
Software Library > Application Mgmt > Applications > click on your application > at the bottom there are 3 tabs [Summary | Deployment Types | Deployments] – click on deployment types > right click your deployment type > Update Content