Tintin,
All you have to do for now to use your cover is make sure you sleep the reader manually with the switch and wait for it to shutdown before you close the cover or put it in the case and you should be fine. The issue seems to be allowing something to break the IR beamed over the screen before it can shut down. As long as you prevent that once it's shut down there should be no excessive drain from anything being near the display so your cover should be fine.
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