I ran into issue that sounds similar to yours, but it started from changing Mobile and IIS settings opposed to licensing.
I had pathing errors after making some changes to the configuration of ArcGIS Mobile. I fixed it by removing all records of past projects in the 'Mobile\ContentRoot\WindowsMobile\XXXX' location, in my case a folder I had named 'Traffic'. I then republished the projects to the web server, and everything worked.
Make sure you back up everything.
Good luck.