We never will see such changes for anything as far out as the hypothetical planet nine. The orbital periods for objects beyond 100AU are measured in thousands o

We never will see such changes for anything as far out as the hypothetical planet nine. The orbital periods for objects beyond 100AU are measured in thousands of years, as far as our observations go they might as well be stationary. Yes, unusual values for orbital parameters are only evidence that something happened in the past, but that thing that happened in the past might have been "close approach with a planet". And as a hypothesis, this is in no way less valid or likely than a flyby with a star.