Ran,
Metropolitan lost nine holes when the Education Department compulsorily acquired the land for new schools. I don't know what is left of the original nine, but I'm told that they lost something pretty special.
Commonwealth lost its 10th hole in the mid-sixties, and I'm told by fellow members of long-standing that something special was lost there as well. The current 11th hole, which has been called by some as the best on the course, which I find hard to disagree with, is also not original, it was installed during the 50's. Other holes to be altered include the 1st, 7th, 6th, 8th and 12th.
Victoria was altered somewhat by Peter Thomson for years, including raising the first green. It's hosting the Open in November, and has been subject to works by Mike Clayton (whose changes I find positive) and TWP as the AGU "Open Doctors".
I'm not sure about all the changes at Yarra Yarra, except I'm told they enlarged the fourth green.
Kingston Heath underwent much work under the guidance of greenkeeper Graeme Grant, most of which I believe to be restoration. The bunker on 11 wasn't, and my sources tell me the club is/was considering removing that bunker.
The firm of Newton Grant & Spencer undertook major changes to the final five holes at Huntingdale, as well as a new par-3 fifth hole replacing the short par 4 there. Reactions to those changes from the pros at the Ericsson Masters were in the main negative. I can't tell you what the membership thinks: Paul Daley might be able to help.