1. Select the master (reference) object and all the instances.
2. Hit ALT + G to Group them (nothing should move when you do this) and now they should all be in a group call NULL. Rename to taste.
3. Select all the instances and make sure they are Instances, not RENDER instances.
4. Hit C to make editable (yes, you can do this to all of them in one go).
5. Now you select all the converted objects (even if they are smaller sub groups - just select the parent, you don't need to drill down and select each sub (child) object) and:
5a. Put them into one CONNECT object and then make the Connect object editable - this will just flatten everything into one mesh - you'll probably have to recenter your axis
5b. With Subgroups still selected - hold ALT and then add a CONNECT object - this will put each sub group into it's own connect object - then hit C to make editable and each subgroup will flatten into its own mesh - again you can do all this in one go on multiple objects and folders.
One snag can be that making a connect object editable can sometimes add a PHONG tag or change the phong settings - so if you are getting shading errors on your mesh, check out the phong angle.