Stan's not sure giving Ford's journal back to Dipper was the right thing to do. He can't act like all the stuff in there's fake anymore, after all, and the kid's already raised the dead after having it back less than a day.
What happens if he tries to confiscate it now, though? Untold weeks of sulking, probably. And Mabel might take her brother's side and turn on him too. He doesn't wanna deal with that.
Besides, if he takes it back, Dipper might come looking for it. Stan's made it too far now. No way he's taking that risk.