I suffer this phenomenon as well.
Occasionally the pen's bottom stops working.
It has nothing to do with the pen's top part (as well as bluetooth pairing).
Disassembling the battries doesn't help.
Nothing helps except waiting for it to blow over, or maybe by restaring.
Annoying as F*ck!
It doesn't feel like its a pen-hardware issue.
I tested it on two sp3 and when it happened on one computer i switched pens and realized that the sp3 was the problem, not the pens.
either hw or sw.