I had a stock merger between Avalonbay and Vivmark. The two transactions on the Schwab website are shown in the top screenshot. I don't recall the type of transaction that Quicken used, but it resulted in Securities Comparison Mismatches shown in the middle screenshot. I changed the transaction types as shown in the bottom screenshot. This cleared the shares mismatches.
I spoke with Quicken support. They escalated it. A higher-level person called me and confirmed that Quicken couldn't process Stock Mergers correctly. I suggested a solution and he said the best way to get it implemented was to post it in the Quicken Community.
The Solution
The process Quicken could implement when the see a stock merger is to enter a Removed transaction if the number of shares is negative and to enter an Added transaction if the number of shares is positive. In both transactions, the name of the security and number of shares needs to be entered.
A Removed and an Added transaction only change the number of shares and does not change the cash balance.