As long as your libraries are installed to your sketchbook folder (typically C:/Users/(your username)/documents/Arduino/library ), they will not be removed when the IDE is uninstalled. If you have for some reason installed things under the arduino install location (Typically c:/Program Files (x86)/Arduino ), then those would be lost, but you should never ever do that, for precisely this reason (and several others).
Stuff installed via board manager is stored in a different location, and is not removed when the IDE is uninstalled.
You should uninstall the 1.8.5 version using the windows programs and features control panel.
Also, the windows store version of the IDE is known to be flaky - it works fine for most people, but a small number of people report strange problems that nobody else can reproduce, but which don't occur with the normal installer version. For best results, use the normal installer (generally, windows store apps are buggier (when they are a windows-store-ified version of a desktop app) or less functional than other available apps for the same task; I recommend avoiding windows store entirely when possible); if I were in your position, I would uninstall both, and then install 1.8.9 using the normal installer - but if the windows store version is working for you, might as well continue using it.