That was actually one of my first mistakes too, and it was on a friend's cockpit ! I thought my heart exploded when it happened. I had read that Amplifone and WG6100 were (and they are) interchangeable. I thought the degaussing wouldn't needed to be hooked up (it's never important with raster monitors/TV's) and since it was a different connector I skipped it. The thing was that my friend has a cockpit and an upright. The upright had (and has) a working (now rebuilt) Amplifone, and the cockpit a non-working 6100,so I thought running the Amp boards on the 6100 CRT could be tried.... Then I had that small burst of smoke....yikes !
I read that it actually doesn't hurt the posistor somewhere and indeed it's been working fine ever since....
I returned everything as was (because I didn't know that then) and have since repaired both.