I just wrote a little bit of code to solve this (I also have several women with more than one Mother trait).Have to start a new game. I tried using my saved game from the last version, but it still shows the long list of mother traits, because I have like 20 kids with my harbinger queen.
Add it in 01dailyupdate.rpy after the lines "for girl in roster" and "for girl in managers" (make sure to keep the spaces, and not to replace them with tabs), then reload the game and pass one day. The excessive mother traits should be removed, as well as the Fertile ones.
Python:
if "Mother" in girl.traits:
changes = 1
while changes == 1:
changes = 0
for trait in girl.traits:
if trait == "Fertile":
changes = 1
girl.traits.remove(trait)
elif trait == "Mother":
changes = 1
girl.traits.remove(trait)
girl.traits.append("Mother")