In other words, if I have Shares accepted and stop my miner for any reason, do I lose all of the shares I was working on?
No.
But, different pools may have a different reward systems.
https://bitcointalk.org/index.php?topic=104664.msg1146110#msg1146110Say, for PPS, when you submit your shares, the pool will credit you directly.
And for PPLNS, the pool will distribute the block rewards among the last N shares. So, even if you have submitted shares, you may not be paid for those shares or you could be paid double or triple or more.