using open() C command in the Nios II

When you see dropped characters, it is due to bytes being written to the serial port faster than they are output at the baud rate the port is using. At some point the FIFO will fill up and you will start losing characters. If just a few bytes are missing you could try raising the baud rate. Otherwise insert delays in your code, after every data line, or after every byte if you UART has a small FIFO. You could also see if your UART (including its driver) and USB<->serial chip implement hardware or software based flow control. See an RS232 tutorial for more info.