The Evolution engines aren't totally broken in, just pre-run. As the engine breaks in over time, the settings will change a little, and that may (or may not) require changes to the low end mixture beyond the range of the limiter. The high speed needle will also sometimes need to be adjusted outside the range allowed by the limiter on it.

Like the other guys have said, I don't disable the limiter on my student's planes unless I have to to get the engine running right.

However, I have seen a couple where the low speed mixture would drift a bit in flight, and one PTS Mustang where the pin sticking out of the low speed limiter would hit the cowl, resulting in the low speed mixture changing in flight. In those cases just removing the collar entirely fixes the problem. I think the problem is caused by vibration working on the mass of the limiting collar, causing it to move a bit.