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I have a project file using .Net 4 (VS2010, properly update) which I opened in VS2013, upon opening with no warning all NI license.licx lines were removed with no warning whatsover.
This should never happen, if something is going to be changed the user should be informed what is happening, especially if it's going to break a build.
This happens to me frequently with VS2012, and only requires re-opening the solution. I haven't yet figured out what causes the license file to change, but agree that the changes are annoying.
As a workaround, make sure to add your .licx files to version control. Then, when you go to commit your changes, the version control system will show the .licx file as changed, and you can just revert it back to the previous state.