If you've updated the days spent in base in basic.cfg and changed back the emblems time, then there's no need to do anything else as milkcows will appear but cause no other issues.
The base time thing is for me the only drawback for the milkcows, there are no other issues they introduce into the game, other than the fact that they exist where they were historically.
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Though actually on typ ix for example you might get long patrols that are expected to be complete with a milk cow.
In this case, use the flotilla.cfg from Real U-Boat 1.44 over the IuB one.
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