The only example i can give you off the top of my head is speed.
The top speed of any given unit within the editor, is dictated by what is specified in its CFG file.
The top speed of any given group of units within the editor, is dictated by the individual with the lowest speed.
So for example if you have a task force, and it has a tanker in it (which would be realistic), the task force is going to be slowed down to the speed of the tanker. (not neccessarily realistic)
You could go in and hand edit the speed and fix that, so the task force goes at the speed you want it to. But if you open the same file in the mission editor, it will rewrite all the speeds you specified to within the above mentioned parameters. Now your back to task forces moving at 10 knots instead of say, 17 or 18.
Just one example, im sure there's other quirks.
edit:
It also bears mentioning that if you have a UI TDC mod enabled that uses a ships speed for ships length in its cfg file to get accurate Range measurements, and start editing MIS files with the mission editor... WHOOOAAA NELLIE! Queue up the
on that one!
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