FTDI USB device not removed after unplugging
I've found the Apple FTDI driver behaves more predictably than the one from FTDI.

Use kextstat | grep FTDI to see which driver you have. On my MBP I had com.FTDI.driver.FTDIUSBSerialDriver (2.3) ... which exhibited the (unwanted) behavior described by the OP.

I removed that driver with sudo kextunload -b com.FTDI.driver.FTDIUSBSerialDriver. 

Next time the FTDI dongle was installed, the apple FTDI driver was loaded automatically. kextstat|grep FTDI reports com.apple.driver.AppleUSBFTDI (5.0.0) ... Now I can remove and replace the dongle and it continues to be recognized by the Arduino IDE.

Hope this helps.