It will not, if the style names are the same.
In other words, if Doc#2 has a Yadda style, and the master doc template has a Yadda style - and they are different format - then the master doc style will apply.
How are you adding Doc#2? InsertFile? Copy/Paste?
If it is a paste, you could try using:
PasteAndFormat(wdFormatOriginalFormatting)
Frankly, while Microsoft has tried for years to get Master/Sub documents working, IMO, they never have worked well. I have tried using Master/Sub and it has never worked well.
Gerry