0. emacs -Q
1. (run-with-timer 5 5 'message "abc\ndef")
2. then activate the minibuffer and switch back to the original buffer
3. after some time observe that only the first line of the multi-line message
   is displayed in the minibuffer

I don't know where this problem comes from, but it's impossible to use
edebug to debug minibuffer-related bugs while the minibuffer is active,
because only an old message is displayed, not the most recent,
when using set-multi-message to collect messages.  So here is
at least the fix for set-multi-message: