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Not a tax pro, but I will give it a shot

1. Suppose I have held 100 shares of XYZ in Account A for more than a year, and then I transfer those 100 shares to Account B, with an ACAT transfer, and sell them. Does the transfer reset my holding period?

It shouldn't. But I would keep a record of that ACAT transfer just to be sure.

2. Suppose I hold 50 shares of ABC in Account A and 50 shares in Account B. I sell 50 shares in Account B, and then another 50, such that Account be is short 50 shares. Net, I hold 0 shares, but one account has +50 and another has -50. Did that second sale count as a short sale, or do I act as if I am net 0?

Account B had 50 shares, you sold them. So you have no shares. You then sell another 50 shares, you have a Short sale. That short transaction remains until you cover that position. The fact that you have an identical number of shares elsewhere doesn't matter, unless you transfer the shares from account A to cover the short
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