To go along with the Grandfather Paradox entry, if Arceus had the Jewel of Life returned to him in the past, he would have had no reason to return to pass judgment on humanity in the movies' present, which further negated the heroes' trip into the past in the first place.
As well as if it was returned to him, and everyone returned to the present, Arceus would not have continued fighting until he recognized Ash. In fact, everything past the Ninth movie (The Darkrai and Shaymin movies) would have been un-written.
Wait... Dawn acquired an item during the tenth movie that, if I recall correctly is eventually talked about and used in the anime. Wouldn't this essentially unwrite pretty much from D&P's midpoint onwards?
It might be the fact that Arceus himself was present at the time, remember, he is a God. Perhaps returning to the present saved them and the past Arceus delayed the time rewriting until after they were safely in the present?
Arceus isn't a god. He's revered as a deity; that doesn't make him one. But more to the point, a probable reason why the alterations had to catch up with the judgment future may be because it was the judgment-era Dialga that sent them into the past, and therefore, past-Arceus restored them to the judgment-era with all of the changes intact, like sealing a crack with putty. You (Dialga) seal the crack (the betrayal past) because it's a crack and it's unseemly, but once it's filled, the crack is still there, it's just that it's now filled with putty and is less noticeable as a result. It's an unconventional way to think of time alteration, yes, but it works. The better question is why there weren't two sets of Ash and co. running around after Sheena had Dialga send them even further back in time after witnessing the first betrayal.
Just a theory here, but maybe Arceus, being the one who created Dialga, can ignore changes to the time stream? Maybe any attempt to change time can be negated by Diagla and Arceus, so even if characters try to use time travel in the show, they only allow it to happen when it needs to. Effectively, Arceus's anger let him ignore a new time line, and once he saw Ash, he became aware of the new time stream, and chose to let it happen.
When you create the entire world and everything in it, I think that allows you to qualify for godhood.
When Arceus is dying, Ash and friends start disappearing. Marcus says it's because without Arceus they wouldn't have any reason to go back in time in the first place, so why is it treated like they're being erased from existence?
Because that group was. True Ash and the others would be fine in the timeline where Arceus didn't attack, but the current set of heroes from the timeline where does are being erased to make way for the new future.
Okay, so Ash swings down and grab the Jewel of Life between his feet, badass for once, yay, and then he waits Pikachu to go bellow him to grab it, worked, but... why? couldn't he have just sent out Straptor or Gliscor and flow down? the prison scene proves that he had his Pokémon with him, and he was holding in the log with a single arm, it just... seems rather ineffective.
What did they use to drown Arceus? I figured it out it's mercury, since it melts at room temperature and they call it "silver water" (that's what they called it, right?)... but then the Tear Jerker page mentions it's silver.
Marcus mentions using silver before implementing the betrayal, which is why the term sticks. There's debate over what it is, but basically any molten metal would be sufficient here.