Thanks for your reply!
I see I have been unclear. My setup:
[ PC ]----usb cable-----[FTDI breakout board]---four wire cable TX/RX/RST/GND---[standalone atmega328 board]
If I wish to switch boards, I remove the four wire cable from the board and connect it to the next. Sometimes that action results in a locked COM port on the PC. In that case, I remove the usb cable from the PC, quit arduino IDE, reconnect usb cable, reopen sketch. This always results in a working setup again, but is more work than necessary (I hope). If I remove the usb cable, I do not use the safely remove hardware option, but that has not resulted in problems yet.
Cheers,
Jack