oh my this could be a few fics, There's a very common Mate/rape theme/plot device in use for SK, often times with these mate/rape themes, kagome's not at all stable, and some times Sesshomaru is more then violent. B/c of this she often hides the kids away from him until they are say 4 or 5 years old youkai/hanyou wise.
Perhaps is the fic your looking for one of these? I know iv'e read more then a hand full like this.
This one is similar to your descriptions, but kagome doesnt just hide them, it's more like she leaves and doesnt know she's preggy until after shes on her side of the well:
In Heat » by Teensie-sama www.fanfiction.net/s/4594954/1/In_Heat
His beast overpowers his will to refrain from taking her and marking her. His decision, to kill her, fills him with regret he cannot fathom. Did he really love her after all? Ses/Kags. R&R Thanks! rated R LEMONS XXX
Inuyasha -
Fiction Rated: M - English - Romance/Family - Chapters: 8 - Words: 24,429 - Reviews: 439 - Updated: 4-26-10 - Published: 10-14-08 - Kagome/Sesshomaru - Complete