Double libraries; in "Program Files" and in "Documents"

Every now and then I run into the problem of having two (identical?) libraries. When the IDE was installed, it made a folder in the Arduino program file, but also in Documents/Arduino. Over time, I somehow have gotten libraries with the same name in both locations. While one may be the originally installed version (in Program Files(86)/Arduino/libraries, the one in Documents/Arduino/libraries may be more up to date.
When compiling a sketch, the compiler will report either an error or will indicate it chose one or the other.
I wonder whether others have this too and also wonder how I got to this point. I would expect the libraries manager to prevent double libs.
Also, I cannot throw away the library folder in Program Files for instance as it contains also libraries that do not exist in the other folder.
Anybody recognize this? What is the best solution?

Sorry, this was a bit stupid. I found the answer.
In order to solve the problem I threw out all double libraries in my Arduino/Sketches folder and then turned to the libraries manager to check out for any updates. Sure enough, the ones that were now single (and outdated) libraries in the Program folder were all updatable.
Problem solved.