Can you please tell me what delimiter you are using to read the flat file ?
Also, the new line character, can you tell us if its \r, \r\n or \n? We can determine this by running hexdump -c <file_name> and examining the output.
Finally, if we know which character needs to be removed, we can use the "Command" in the Flat File Reader to remove it using a shell command -
delimiter we used is | (pipe) and new line character is \r \n
Assuming that our underlying OS is Linux, I think we should be able to use the Command in the above link to specifically remove them using commands such as sed.
For example, sed 's/\r\n//g' <file_name>
This should remove all instances of \r\n and then feed the resulting output data as input to the DIS to process.
Please note that this is just an example and one of many possible solutions. Also, there might be other commands like tr too.