Watch this scene from the movie No Way Home carefully. Doctor remembers the moment he disappeared from Tobey's timeline very clearly. Let's go back to the past, the ending of Spider-Man 2. Tobey's Peter was trying to stop the doctor's fusion reactor, and the doctor had grabbed him by the throat. In short, he was about to break his neck, but just then, Peter gave him a speech about the doing the right thing, and the Doctor's mind had changed. Frankly, it's very strange that the doctor's mind has changed, especially when the arms are controlling his brain. Therefore, if you watch this scene carefully, you will notice that the facial expression of the doctor suddenly changes. I guess that was the moment when Doctor went back from Tom's timeline to his own timeline.