If you clock in on a work item, and then walk away from your computer—perhaps to take a phone call—you often need to “resolve” the time you were away by either subtracting it from the current clock, or applying it to another one.
By customizing
the variable org-clock-idle-time to some integer,
such as 10 or 15, Emacs can alert you when you get back to your
computer after being idle for that many minutes1, and ask
what you want to do with the idle time. There will be a question
waiting for you when you get back, indicating how much idle time
has passed (constantly updated with the current amount), as well
as a set of choices to correct the discrepancy:
What if you subtracted those away minutes from the current clock, and now want to apply them to a new clock? Simply clock in to any task immediately after the subtraction. Org will notice that you have subtracted time “on the books”, so to speak, and will ask if you want to apply those minutes to the next task you clock in on.
There is one other instance when this clock resolution magic occurs. Say you were clocked in and hacking away, and suddenly your cat chased a mouse who scared a hamster that crashed into your UPS's power button! You suddenly lose all your buffers, but thanks to auto-save you still have your recent Org mode changes, including your last clock in.
If you restart Emacs and clock into any task, Org will notice that you have a dangling clock which was never clocked out from your last session. Using that clock's starting time as the beginning of the unaccounted-for period, Org will ask how you want to resolve that time. The logic and behavior is identical to dealing with away time due to idleness; it's just happening due to a recovery event rather than a set amount of idle time.
You can also check all the files visited by your Org agenda for dangling clocks at any time using M-x org-resolve-clocks.
[1] On computers using Mac OS X, idleness is based on actual user idleness, not just Emacs' idle time. For X11, you can install a utility program x11idle.c, available in the UTILITIES directory of the Org git distribution, to get the same general treatment of idleness. On other systems, idle time refers to Emacs idle time only.