Valve clearance, dented shims, again

Once, about seven years ago when I bought the car, I had to flip some shims to solve a really loud ticking noise. Thanks to the advice of this forum. The problem was solved.
Now, twice, the ticking noise is coming back. Not so loud, but noticeable.
I am currently replacing the head gasket due to oil leakage, so the opportunity to inspect the shims presents itself. I now find shims dented on both sides. No more flipping.
Is this an issue that has occurred to any other members?
I am following the service manual procedure for calculating the replacement shim size to solve excessive clearance (Section 12.1 page 15). This involves the existing shim size, but I can’t measure this as my micrometer goes in the dents on both sides of the shim and gives a nonsense reading. If the shims were dented on only one side I could use those measurements, with the clearance by feeler gauge, to get the correct shims.
My question is, can I use the measurement of the original thickness of the shim, the remaining rim that is, as the size of a replacement shim? I can measure that accurately. In fact, all three problem valves have the same size shim, 100.5 thou.
Replacement shims are cheap and readily available. Why did I flip the shims in the first place?
The motor is a 1992 4.0 litre.

If your micrometer can fit inside the indent how about using a decent thickness of feeler guage on one side and simply detract the difference?

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Good point. Will try.