I regularly delete all zero byte and temp files on the windows partition using D7 and have never had a problem. However I've always understood that the best advice is "do not delete temp files that are less than 24 hours old" to be on the safe side.
Since I always have a system image backup I don't worry about it too much.
I also clean up system files using the sagerun/ sageset commands that give additional options but I guess you know that already! Just in case you don't here's the info: