Hi Metman,
Just FYI, nothing in a custom mission can ever change the actual dynamics of the vessels or the oceansystem or any other 'hard coded' game feature, and hence cannot negatively affect any stock missions.
The only instances where things change, is with official game patches, or with externally made patches, like the superpacks.
These have been reported to have an affect on things, since clearly they change the actual ship behaviour of the ships in question, or the draft, and such..
But no custom mission can do that, they don't work like that and they are just scenario's that
use the game content, not
change it.
So you need not worry about that.
Regards,
Fred