There's a setting that you can change to increase the limit before the data is exporting in csv format: RowLimitForCsvInsteadOfXls
On the server you can change the limit in the QVS settings.ini file
In Qlikview Desktop you can change this with an 'easter egg' setting. In the Help menu select About Qlikview. Then right click on the Qlikview icon in the lower left corner. Find the entry RowLimitForCsvInsteadOfXls. You can then increase the value from 65500 to a higher number. Note, this may cause a performance penalty on your server.