You should only see this when opening a file from the Accountant's File Transfer service. However, you may also see the message when:
Note: Before you start, determine what version of QuickBooks Desktop your client is using.
Solution 1: You are using the same version as your client
Solution 2: You are using a different version than your client
Solution 3: Minimize the chances of data damage when not using the Transfer Service
3rd party transfer services such as Drop Box, dragging & dropping using Remote Desktop Connection or other "portal" services can truncate or short-length a file. To keep this from occurring send the accountant transfer file to a compressed zip folder before using the transfer services.