I am having similar problem. All transactions are entered by hand. I have 2 different accounts holding the same security but for reasons lost to the mists of time I set them up as 2 different securities. I tried editing the transactions in 1 account to change the security and MD can no longer calculate the cost basis.
MD 2017.5 (1639)
Mac High Sierra
Screen shot of cost basis report attached. There should be 25 years of cost basis here
Recently I worked through this issue after moving to MD 2017 from Quicken on Mac. Quicken forced securities to be designated either taxable or not, so I named the same security different depending on if it was in taxable or not. So to undo that in MD:
1. In a non-taxable account register, sort transactions by the security to be merged, replacing it with the security name used for the taxable account. This is to prevent upsetting lots in the taxable account.
2. Verify there are no transactions using the name that is being replaced before deleting it from the securities list.
3. In the securities list rename the one you’re keeping, if desired.
Tom Freeman on 31 Dec, 2017 09:07 PM
This happens somewhat frequently when downloading from multiple brokers. Different brokers will sometimes fill in the security ID differently and if not caught will create two unique securities within MD. Part of the download process, is if MD does not recognize the security, to prompt for a security match or none of the above.
Christoper's fix is a good suggestion. On the next download into the edited account MD may not recognize the downloaded security as the edited security and you should be able to match it with the recent edit and after that subsequent downloads should recognize the correct security.