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buying back a covered call
user
if you buy back the now itm calls, then you will have a short term loss. that pair of transactions is independent, from a tax perspective, of your long position (which was being used as "collateral" in the very case that occurred). i can see your tax situation and can see the logic of taking a short term loss to balance a short term gain.  referring to d stanley's answer, #2 and #3 are not the same because you are paying intrinsic value in the options and the skew in #2, whereas #3 has no intrinsic value. of course, because you can't know the future, the stock price could move higher or lower between #2 and #3. #1 presumes the stock continues to climb.
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