I am not sure if there is any direct option, but you can use annotation() to draw a line on the figure window such that it appears on the axes at correct locations. Following code shows an example
figure;
chans = 10;
for subplotN=1:chans-1 %plot first set of time-series
x = 1:2841;
y(:,subplotN) = randn(2841,1)*50;
end
y(:,subplotN+1) = randn(1,2841)*1e6;
s = stackedplot(x,y);
pos = s.Position;
xlims = s.xlim;
line_locations = [500 1000 1500 2000 2500];
line_locations_norm = interp1(xlims, cumsum(pos([1 3])), line_locations);
for i=1:numel(line_locations_norm)
annotation('line', ...
[line_locations_norm(i) line_locations_norm(i)], ...
[pos(2) pos(2)+pos(4)], ...
'Color', 'r', ...
'LineWidth', 1);
end
