As far as I am aware, every Tunnel between Glenbrook and Marrangaroo were skinned as well as being lowered for the 1956 Electrification.
I have an idea further works were carried out around the time of the Standard Gauge was opened between Sydney and Perth to accommodate the carriages on the Indian Pacific and interstate freight wagons.
Clearances have always been close as was found when fluorescent lighting was installed in Number 10 tunnel during the laying of the concrete road bed as they were struck by a passing freight wagon when it oscillated a bit too much.
From vague memory I think a 60 class Beyer Garret was prohibited from passing through the Capertee Tunnel due to its restricted clearances.
In one of the forums there was a picture posted of the Overbridge between Wambool and Brewongle which clearly showed how the brick pillars of the bridge has been cut back to increase the gap between them.
I can think of three tunnels that are today as they were before 1910 and one is on the Lithgow Zig Zag (unlined?) and the other 2 on the Newnes Juction to Newnes into the Wolgan Valley, one being the very popular Glow Worm Tunnel.