Is there a danger to either the uploading computer or an Arduino board if the Arduino is still being powered at Vin while uploading a sketch?
There should not be. If Vin (the voltage after the reverse polarity protection on an Uno for example) is > 6.6V, than the power source autoselection circuit will route 5V from the regulator to the board instead of a little under 5V from the USB input (a little under due to the PTC resettable fuse between the USB socket and the 5V line).
Thank you