> So the problem is in (org-user-idle-seconds), which in my window system
> boils down to a call to (current-idle-time). It should return 0 after
> answering the prompt, but in my system it keeps counting up. At this
> point I stopped investigating since that function is defined in C.
>

I have investigated this a little bit further and it seems that reading
a character with read-char only resets the idle timer if the SECONDS
argument is nil (which is not the case here) . I reported it as a bug to
bug-gnu-emacs@gnu.org, but it seems there is a reason for that. See
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=54371

> Since this bug is already old and I have not found much information
> about it, I assume that in most systems answering the prompt does reset
> the idle timer and this bug does not occur.

It also seems to happen for all systems, so either much less people than
I thought use this feature, or there is something else that makes this
bug particular to my setup, although I can't think of anything else.

> As a quick fix for those
> systems where this is an issue, we could reset the idle timer ourselves
> after the prompt in org-resolve-clocks-if-idle.

I have thought of a better way to fix this, and currently there is no
way to do reset the idle timer with Elisp anyway. I attach the patch: it
just cancels the timer before prompting the user and sets it again if
needed after the prompt is answered. What do you think?