One of the more depressing things in Timeflight (other than the script and the effects of course) was the fake-out ending in which we were led to believe that Tegan had been left behind at Heathrow. It was a natural enough assumption on the Doctor's part; she'd been going on pretty much non-stop since the moment she set foot on the TARDIS about wanting to get back to Heathrow and her job. When the TARDIS ended up there on an unrelated matter (for those who haven't seen the story in question - the Master summoned them there for Vaguely Racist Hi-jinx in Pre-History) it was only logical that he'd think she wanted to stay there. It is a little odd, however, that he just took off without confirming that (or even letting her that know he was leaving for that matter) but it's not as if the Doctor leaving without saying goodbye was unheard of. Perhaps he'd just had a peek at the time scanner and knew that he'd see her again in Amsterdam just as soon as she'd finally changed clothes and gotten a decent haircut.