Can folks just verify that all types of upgrade instruments (GPU, RPU, miles+cash) should be returned/refunded when a ticket with a confirmed upgrade has to be changed before departure?

I know that's supposed to be the case with waitlisted upgrades that don't clear, although I've had more than my share of challenges getting the cash portion of upgrades refunded. However, for the first time I have to change a ticket that has confirmed upgrades (one using RPU, one using miles), and want to make sure I don't just lose the instruments if the ticket is changed. Or if there's some procedure I should call to "undo" the upgrade before making a change to it.

Alternatively, if there is R upgrade space available on the flights I want to change to, is there a painless way to just keep the upgrades in effect while the flights are changed?

Yes you get them back. If you make the change over the phone you can just tell the agent you want to upgrade the new flights and they'll re-apply the instrument for you. I don't know how much pain that would cause... doesn't sound like much .

Although in practice they'll likely take a different instrument and you'll have to request a redeposit of the original.

octeckels and I have had to request several award redeposits recently. None have shown up automatically, but all have appeared back in the account within a day of submitting an award redeposit request on the website.

I just went through this today. TATL flight confirmed with GPUs. Changed the flight to December and they had to reissue it. Original GPUs were redeposited and new ones drawn (per the agent).