Just this month I had this scenario with five of my mutual funds. Most of my class C shares were converted to class A, but a small number of shares of each fund remained as class C.The problem is that the Mutual Fund Conversion transaction only converts all shares from one class to another.My solution to this was to first use a Remove Shares transaction for the remaining class C shares first with a trade date one day before the conversion. I then entered the Mutual Fund Conversion transaction for the balance of the shares according to my trade confirmation on the date it occurred.Afterwards, I deleted the Remove Shares transaction I temporarily entered prior to the conversion and balanced the shares and market values to my statement, everything worked out near perfectly. The only thing I had to do was modify one converted lot of converted shares at the 6th decimal position, to balance the shares to my account statement to adjust for a share rounding discrepancy.
Quicken will use a first in, first out approach to convert shares of the old fund to the new fund, and stop when the number of new shares added to your account matches the:amount you entered in the "Shares of new Fund" field.