I thought about the stock split and corporate spin off approach, but I think although it may save some drudge work, it is more complication than I would want. But to each their own...
If you decide to go the brute force method - entering a Remove Shares for each security you will be halving, here is how to do it.
Use the Shares Transferred Between Accounts transaction type. Select One Security, enter the security name, the halved number of shares you will be removing, and select Lot Identification. Click the Specify Lots button.
Then in the Specify Lots dialog, type in the halved share amount for each lot of the security. You may find a calculator or Excel handy if you need help to divide the available shares by 2. Note - this dialog is labeled Specify Lots Sold in This Transaction, but it's really for specifying lots removed.
Repeat for each security. Be sure to take a back up before starting and as many back ups as you feel necessary as you proceed through all the securities.
Sorry for taking such a long time to reply, but I wanted to wait till the end of the quarter to get my mutual fund statements in order to try to get the correct basis for my holdings. Thanks so much for the creative and thoughtful responses. In the end I decided to use Q.Lurker's approach and I am glad to report that it seems to have worked well. A few things I learned in the process. The first that when you do a stock split for a fund in one account Quicken does split the same stock (or mutual fund) if it is in another account. Also, if you try to delete the split transaction in the second account Quicken will delete it in the primary account. I haven't worked through this yet, but it was a relatively small problem compared to my initial issue.The other thing I learned is that each step of Q.Lurker's process should be on a different day. Quicken does not seem to be able to let you split and transfer securities on the same day. Thirdly, heed Q. Lurker's advice to back up and back up often. This is a complicated process and it is really easy to make a mistake. It was great to have back ups so I did not need to go back to step one.