This message is referring to the ACH file that is created when processing EFTs.  The message is stating that the process is going to overwrite this file with the new payroll information.  It is ok to click YES if you have already uploaded the previous payroll to the bank, if you have not then you will want to click NO and upload the file prior to processing a new payroll. 

If you upload your EFT information manually to the bank then it is ok to click YES and overwrite the file.