Near the end of the game she always disappears for me and I beat the game twice
And I beat the game 3 times, on top of doing save scumming during run 3 to check out different things.
Run 1 was a pure love run where I blocked every NTR event, but I did not take the hypnosis book. Atelle didn't ever disappear.
Run 2 was a NTR run focused on the grandson, I took the hypnosis books to make things simpler, Atelle started disappearing. I put the hypnosis book back, Locke's events started to trigger, she never disappeared again.
Run 3 was a run meant to do stuff with the Adultery ending. Didn't take the hypnosis book. Got Atelle to fuck every other guy except the grandson, she never disappeared, but she did have some days where she had NTR events in every single time slot.
Did some save scumming stuff during run 3 to see how ends up at the Treasue Hunt and Training Camp event and to mess with the nun events... and I never had a situation where Atelle disappeared that I can remember.
For clarity, I took the 1.02 version in the OP and applied the 1.04 patch on it directly. Dunno if that does anything or not... but I genuinely think that Atelle being completely gone from the map is a bug. It has one absolutely consistent trigger, but I suspect that there are others that might trigger it... However, I can't be assed to try and figure it out. I'm done with this game and I'm not being paid to be a bug tester or anything. XD