Just because the shares are uncovered shares doesn't mean that the mutual fund company is not tracking the cost basis. In this case is seems that the cost basis of the uncovered shares is $6k. If the $6k figure is correct, adding that to the $45k of cost basis for the covered shares gives a total cost basis of $51k. With a current value of $50k, you have a $1k capital loss.
You only have a realized gain or loss if you sell the shares. If you move the shares in-kind, you don't realize the loss and your current cost basis transfers to the new mutual fund company. Of course if you are changing mutual funds, that involves selling the old funds (realizing the gain or loss) then using the proceeds to buy the new fund.
Presumably these mutual funds are not held in a qualified retirement account where the rules are different.
