Sorry to be posting back to this so late, I've been away for a week or so.
I took my dash apart and checked all my wires, and put everything back together.
I now no longer get the thump when removing the empeg while playing. I must have had a loose wire somewhere that I couldn't find, but that got straightened out when I checked them all.
I pulled it out once while playing to see if there was any issue. It didn't thump then, so I've been doing it ever since. I was just mentioning it to see how other peoples empegs behave.
Again, I assume that in my case it was just a wire that was loose, but not obviously so. Such that when I checked all wires, I fixed the looseness without noticing it.
Thanks for your responses...
-Trevor
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Mk 2, Green 12GB 080000349
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-Trevor
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Mk 2, Green 12GB, Tuner, 2.0b11, 080000349