I guess you should manually clean them out, but be cautious about remove the system files which related to or shared by other applications. Otherwise, OS will prompts a missing file notice everytime you boot the computer!
I manually cleaned out my .....\Temp folders a while back. No harm done. Right now, most of \Temp folders are empty, including the folder in the account that I use daily.
I'd shut down all my applications, empty the \Temp folder, and reboot.
Safest thing to do would be to move all of the files into another folder ( like C:\testing ), reboot, and then make sure everything goes alright. If everything goes as it normally does, then you can delete the files...
If you're afraid to do it manually then running disk cleanup (right click on c: in my computer - click Disk Cleanup) may delete those temp files as well and won't delete anything required for Windows to run.
But most of the time anything in a Temp folder is safe to delete.
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