Yes, I would change the ST box amount and the LT box amount.  I work with complex hedge fund K-1s all the time and this is not an unusual occurence.  I also concur with your assessment that the determination of the affect of Section 1061 has already been done at the fund level.  There is some uncertainty in the application of the law as to whether the holding period must be met at the fund level or partner level or both.   Good luck.