Why are you removing shares? Did the stock have a reverse split or corporate reorganization? How were the shares added in the first placer? If bought the shares, why to just sell them? If the stock no longer exists, you can sell the shares for a zero gain.
I would look at the beginning of the account register to see if you have any transactions that are in light gray. These are placeholder transactions that will get added to auto-adjust the share or cash balance to what it is supposed to be (typically as reported by the brokerage house)I think you will find that when you enter your Remove shares transaction, a placeholder is adjusting to compensate for that so it appears that nothing has changed.I don't know the particulars of your account (manually entering everything, first time download, etc.) The answers to those questions will determine as to whether you need to delete the placeholder or replace it with a regular transaction that doesn't auto-adjust, etc.