> I almost always choose 'k' (keep) and it is often not responding after the
> first or several presses. But as Samuel Loury pointed out, I'll try
> pressing ten times at least, the next time it happens.

IIRC, pressing 'k', even a lot, did not work. I realized that i might be
linked to the fact that 'k' asks for some minibuffer input and this
input is waited in the other frame. And when emacs is waiting for some
minibuffer input in one frame, there is nothing I could do to get the
control on the other frame.¹

What I am suggesting is to press a lot 'i', until org-mode releases its
grasp on the other frame. You notice that it is so when the letter 'i'
gets written in front of you :-). Then, when org-mode let you go, you
can run M-x org-resolve-clocks and you will be able to press 'k' this
time.

I hope this is clearer this time.

Good luck :-).

¹ Actually, there is one way. Send the SIGUSR2 signal to emacs (pkill
  -SIGUSR2 emacs) so that it starts the debugger (in your current focused
  frame), then close the debugger and re run manually M-x
  org-resolve-clocks. SIGUSR2 would have enabled the debug-on-quit, so
  disable it with M-x toggle-debug-on-quit