Should I sell long position stock with profit or short position with loss? (same company)

I will need to sell some of my company stock end of this month. I have both short and long position stock. The short position stock are losing about 10% and the long position is right now between 20-40% profit.

If I sell now the most recent stock, and the stock goes up, I will have even more profit to realize in future. I may have a year of selling short at a loss but when the profits come in future years, I may have to pay more tax and the loss of this year won't count for next year.

So, what should I do?