Reference Edits

One crucial thing with referencing is that the Reference Edit List isn't just a macro that's run in the order you performed the actions. Instead it's grouped and more importantly applied by function types. If you open the refEdit List up you'll see the grouped calls:

: setAttr
: addAttr
: connectAttr
: disconnectAttr
: deleteAttr

To get to the edit List open the referenceEditor then File > List ReferenceEdits

This is a contentious issue and has been bought up on the Autodesk Beta forums many times. In Maya2011 there has been some fixes to this to make it more intelligent. Try the following in 2010 and then 2011.

Make a cube and reference it into a new scene, run the following and save this new scene. Now open the file again...

import maya.cmds as cmds
cube=cmds.ls(sl=True)[0]
cmds.addAttr(cube, ln='Test')
cmds.deleteAttr('%s.Test' % cube)
cmds.addAttr(cube, ln='Test')

So we've added an attribute 'Test', then deleted it, then added it again in a referenced file. Now this looks like a stupid thing to do, but lets say you're using attributes as markers in a function, maybe exportFlags etc. In 2010 if you look at the edits you'll see the addAttr, then under that the deleteAttr.... regardless of the fact that the last action was to add the attribute again. When the scene is saved the new attribute won't be there because the delete was the last thing in the editList. More over, unless you go and remove that deleteAttr from the editList itself, you'll never be able to remake it.

2011 has a fix for this case.