you can use the better pregnancy 1.6 option to remove the belly when you take them out as your companion. I was having this issue but one of the npc's left me and the problem went away. Not exactly sure how the issue got resolved with my save like that.
The official vin_pregnancy mod have 2 manual scene what could be help in this cases:
'force_birth'
This one start the labor and end the pregnancy.
'end_pregnancy'
This one simply end the pregnancy.
(Usage: press 'Ins' button and copy&paste the scene name without extension like above)
Of course neither scene has the 'magic' code ('Actor.setMorphValue(Genesis8Female__PBMPregnant, 0)') for the belly removal, but in some cases could help if succesfully pass through the AI at midnight.
Otherwise if you're a hard nugget and able to find your character under 'saves' dir (save the game, textsearch on the saves dir with the desired character firstname and selecting the latest modified file), you can look for the "PBMPregnant" string in the characters file and edit the num value to zero as above.
Much easier way is to generate a new body (only) in the 'Edit appearance' character editor (set actual age, and beauty on the small panel before you give it a go).