How are you exporting data? From a report, or the Export Accounts function, or an Excel Direct smartfinder?

If you are using an Export functions such as Accounts or Batches, you may get the 'error - data may be lost' if you have Excel 2007 because the created exported Excel file is a low-version file (so we don't prevent people with older versions of Office to use the function). There should not be any loss of data, unless there are more than 65535 records as mentioned above.