The LAS files can be stored with the Project Folder - that is a setting that you want to copy the files to the Project file or not - That can be found under Support - Options - Point Clouds and is a check box that says

The second thing that says Point Cloud Functionality has been disabled - Check your license information in Support License Manager - maybe you lost connection to your Security Key / Network License and therefore don't have a License to run the Point Cloud stuff active or something like that. Failing that I would reboot and see if that clears the issue. Let me know if either of these work / don't work - I may have to get the Techs on this one as I have never seen that message personally
I cannot tell you why the Point Clouds disappeared from the project - that looks to me like the Project lost connection to the SDE Database used for the Point Clouds for the project - I cannot tell you how that happened
Let me know if you can recover the functionality or not, and I will discuss with the Techs on Monday am.
Alan