Note: As this merger completes, and the broker migrates data, the supported import methods will change. Those that were previously able to use BrokerConnect will lose access to this import method.
Since you will receive two separate 1099-Bs - pre-merger 1099-B from ETrade, and post-merger 1099-B from Morgan Stanley - we recommend that you have two separate account tabs in TradeLog: one for the pre-merger ETrade data, and one with the post-merger MS data. This will make the 1099-B reconciliation easier.
You'll want to import up to the merger date in the ETrade account.
Then, press the "Open" button to view/verify your open positions in the ETrade account, and click the "Transfer Open Positions" button to transfer all the ETrade open positions to a new account tab for Morgan Stanley. See: Transferring Open Positions.
Then go to the Morgan Stanley account tab and you can continue to import your transactions from the post-merger date onward, by following these import instructions: Importing from XLSX - Morgan Stanley
If you are not yet able to download your new trade history from Morgan Stanley, then you should be able to import via a CSV file from ETrade: Importing from a CSV File - E*Trade Financial