Can Uno be Programmed with Both USB and Vin Present?

My project runs from a regulated +9v going to Uno Vin and I'd like to debug the code while its powered from the 9V. If I plug in a USB cable to reprogram it with my MacBook, is there an issue because it's still powered by 9v? I read that the Uno uses the higher of its input voltages but still not sure if its okay for the onboard regulator and my Macbook USB port.

Yes, it will be fine. The UNO disconnects USB power if Vin is higher than 6.6V.

At the top left of the schematic you will see RN1A and RN1B (10K Ohms each) used to diviide Vin in half. This goes to one side of a comparator (U5A). The other side of the comparator goes to the 3.3V rail. If the comparator determines that Vin/2 < 3.3V it will gate a FET to connect USBvcc to the +5V rail.