That's pretty much how it works, it does take a few days for her to realize she's pregnant. You might be able to use something like Cheat Engine to clear the pregnancy state and continue using this save.
Thanks guys, was just wondering if this was the case.If you haven't completed the Great Adventure (or used the succubus vial with the FFF-mod), if Imouto gets a creampie during the night-scene, a hidden "implantation" switch gets turned on and a pregnancy timer starts tallying, increasing by one every day. When the timer reaches 3, she's at the point of no return, barring use of Cheat Engine, or completing the Grand Adenture that very day, and she goes into the pregnancy ending, good or bad.
Before the pregnancy timer gets to 3, using the After Pill resets the "Implantation" and "Pregnancy" flags to zero.
Edit: You're stuck on a Saturday? Perhaps you can finish the Grand Adventure. The magic ritual also resets Imouto's pregnancy counter to 0, and locks it at 0, barring mods.
I don't mind starting an old save, just wanted to know how in-depth/complex the system was. Very cool.