So you have the following structure;

Top Level Assy

     Sub Assy 1

          Part 1

          Part 2

     Sub Assy 2

          Part 3

          Part 4

I've made a drawing of Sub Assy 1 (BOM and drawing border all point towards this sub), but the drawing also has a single view of Top Level Assy used for reference.

As Sub Assy 1 & 2, and the parts within them, are very similar, I've just copied and pasted the drawing of Sub Assy 1 and changed the references so it now looks at Sub Assy 2 (And also still looks at the common Top Level Assy).

This is all well and good and I've been changing the references of copied drawings for years. The problem I'm having today is that when the drawing opens after just changing the references, it also seems to replace Sub Assy 1 with Sub Assy 2 within the Top Level Assy!? (Are you still following??)

To sum up, I'm ending up with a Top Level Assy that now has 2x Sub Assy 2's in it? I've never seen this before and I'm wondering whether there's a sneaky little check box I don't know about?