As to the Knox warranty bit, it probably CAN be un-tripped, however, no-one knows how to do it (yet...?) ...
As you may know, a working, Knox-resetting Odin package for one of Note 3 variants leaked some time ago (heh don't get too enthusiastic, it does work only on the specific variant of Note 3 with specific bootloader version...). This seems not to be very helpful, however, it confirms that resetting Knox IS possible (at least on Exynos based devices). It also confirm that Samsung did not tell us all the truth, stating that the Knox is absolutely unrecoverable, because it is based on e-fuse (so it gets physically blown when Knox is triggered) - it seems that either e-fuse is a myth or there are some "substitution" e-fuses included in the hardware.
But as for now, it is true that you unfortunately cannot do anything with the triggered Knox (BUT there is a chance that Samsung service centre won't notice that... there were also ideas such as putting the device into microwave oven for 2-3 secs so the device will be damaged in a way making it impossible for samsung to check the knox status, but they shall be considered as illegal...)
And as to your issues with the device - have you tried adding:
to your build.prop (or changing the value from "true" to "false" if the property "ro.securestorage.support" is present there...).