The safest thing to always do is backup your entire Runtime library in a secondary location or on another drive. I have always used the a magic working Runtime directory of my own creation and merely added it to the library after installing new versions of Poser. As long as you always put in the same location on your drive where you started, (meaning my original location was C:/MyRuntime/) then I can move it to a new computer even and still as long as it is in C:MyRuntime, after installing to Poser, Poser can find everything. Now should I put it C:/MyRuntime/newfolder - I'm screwed and Poser won't be able to find associated textures or geometries. But making and using your primary runtime in an external location from Poser's program files will ensure it never overwrites them. And it's easier to back it up.

Hope that tidbit helps a little. As everyone says, as long as you keep existing preferences, it should not ever wipe out a Runtime but...but...but...crap happens. And 11+ is super glitchy at times so I wouldn't trust an install. Yesterday my icon buttons at the bottom of the library window reverted back to the little button buttons for about ten minutes and the went back to basic icons. I don't even know what to call that. I thought I was losing my mind for a minute. But it did it. Hasn't since. What caused it? Who knows. Poser 11 gremlins I suspect. Point being - don't trust it, back up your runtime.