That work around isn't really necessary. As I mentioned, you can start your secondary mIRC before closing the first. This will cause the new mIRC to read the changes, and the old mIRC will change it back, however, the changes don't matter since when the new mIRC closes, the "new" settings will be resaved.
alias change_ini {
writeini mirc.ini options <item> <new-values>
run mirc.exe | .timer 1 3 exit
}
