kindlepdfviewer doesn't touch the root file system, so it can't do permanent damage on its own. However, it might use up too much resources for some documents (like those which are composed out of 5000x5000px images, to give an illustrative example). This might bring down Amazon's framework with it (hit-and-miss-decisions when out of memory). Nothing a reset wouldn't fix, though.
I don't know much about kite, but it will install a boot-up script, thus will modify the root file system.
When you said "reset", what did you actually do? You _did_ hold the power slider for about 20 seconds, right? Just "turning it off and on again", i.e. short duration slides, won't fix a stuck userland.
Just don't let your battery go fully empty. In the worst case, you should be able to de-brick your device (look up the debricking instructions) - it's a bit of a hassle, but it will always work on the K3 (except of course when the hardware is broken, which can't be done in software, at least not that we know of).