Check out "doc uiwait". Basically, you will just change the above to:
for idx = 1:length(missing_sigs)
mis_sig_no_tok = strtok(missing_sigs{idx},'>');
mis_sig_no_tok = strtok(mis_sig_no_tok,'<');
gui_handle = ResolveMissingSigs(mis_sig_no_tok);
uiwait(gui_handle);
end
The loop will continue as soon as you close/exit your GUI. You can also have the loop continue after a set amount of time. For example:
uiwait(gui_handle, 10);
will allow the loop to continue if you close/exit the GUI or after 10 seconds.