With a big thankyou (as always!) to Chad, one of the support guys at TMS, our SolidWorks supplier.
Draw a line in a sketch in the part connecting the two centres. Back in the drawing, ensure that sketches are visible and snap the section defining line to the sketch line.
(did forget to mention that the section view I created is taken from a detail view)
Cameron, please show us a picture of what you ended up with, I have an idea, I just wanted to see it.
click on a line in your drawing. then go to tools>align drawing> and try the options there.
Show temporary axes in the drawing. View->Temporay Axis
Sketch a line in the view you want to Section
RMB over center of hole, "select other", choose "Axis" , ctrl-select the line, add coincident constraint.
Do the same with the other hole and thel line
Your sketched line will now always pass through the centers of the holes