MickPF:
Since a library update (oh god, I've forgotten which library, but it doesn't matter) the library manager generated a message for an available library update. I changed to the "Library Manager", selected the affected library and looked in the "Version Selection List". But there was no newer version available.
Actually it does matter which library. If you would provide specific instructions for how to reproduce the issue it would make it much more likely that you get help and also make it less work for us to help you. It would only take a few seconds for you to check which library it is.
MickPF:
Maybe the manager compared the file creation/modification dates?
No, it doesn't work that way. It compares the version value found in the library's library.properties file.
MickPF:
One day I found the same libraries (some of them with different versions) in the installation directory "/opt/arduino-1.8.4" and in "${HOME]/Arduino/libraries"!
The Arduino IDE comes with a set of "Built-in" libraries so it's normal to find those in the libraries subfolder of the Arduino IDE installation. When you install a different version of one of those libraries via Library Manager it is installed to the libraries subfolder of your sketchbook folder (which I'm guessing is this ${HOME]/Arduino/libraries you mention). The library version located in the sketchbook folder will take include priority over the one in the IDE installation folder. If you turn on verbose output during compilation in your preferences and then examine the end of the output in the black console window at the bottom of the Arduino IDE window you will see a message when there are multiple files found for an include in your sketch and which of those files was used.
You haven't provided enough information for me to be able to give you a specific explanation of your problem so I'm just going to have to take a wild guess and say it's this:
you will find more information at the various other issues and pull requests references to that issue report.