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Don't know if it's particularly what you are looking for but in "Far From Home" episode of Justice League Unlimited the League are taken to the future to help the Legion of Super-Heroes. The Legion think that Kara is going die because records show that one hero never returned but in the end Kara chooses to stay in the future willingly.
Some possibly relevant examples would be:
- On Doctor Who in "Aliens of London" where the Doctor took Rose a year into the future and, from the perspective of her family, she'd been missing for a year.
- Possibly Star Trek: The Next Generation in "Yesterday's Enterprise with the Enterprise C. This was a bit of a more complicated case since had it remained behind the Enterprise C would have been destroyed anyway, but instead it disappeared and reappeared in the future.
- Goodnight Sweetheart had a Historical In-Joke that Jack the Ripper went missing because he travelled through time to the present and got hit by a bus.
- Eureka has Founder's Day where Trevor Grant travels from the past to the present and is now missing from history (altering the timeline).
If you have the interest, then I don't see why not. Looking at the (admittedly long) existing Time Travel Tropes, this seems like it's covering a valid trope in time travel stories which doesn't look like it's being covered at the moment.
There isn't a trope page for it, but this is a key plot point in Kaliane Bradley's "The Ministry of Time." The Ministry selects people from the past who disappeared from history and brings them to the present. The justification is that they probably were about to die anyway — but the Ministry admits bringing people forward might be why their fates were previously unknown.
Edited by TheGreaterFoolDuckTales (1987) and Star Trek: The Next Generation are listed there.
The Time Travel Tropes list misleadingly describes it as "Going forward in time erases you from the timeline."
(Oops, thought this was Trope Finder for a moment.)
Edited by VehekThe finale of Mirror, Mirror (1995) has the Old Man permanently disappearing... because his younger self just managed to warp to the presentnote and decided to stay there.
Edited by Medinoc "And as long as a sack of shit is not a good thing to be, chivalry will never die."In the Teen Titans (2003) episode "Teen Titans S 2 E 1 How Long Is Forever?", Starfire travels twenty years into the future and witnesses the Bad Future affecting her team-mates resulting from her absence in the present.
Dragonflight, the first of the Pern novels (by Anne Mc Caffrey) has this as a major plot point - in the present day, there is only one weyr of dragons and their riders, with all the others having disappeared mysteriously about 400 years prior. Turns out the protagonist figured out that dragons can time-travel and went back to get them in order to bring them forward to the modern day when they'd once again be needed.

A Facebook post posed this question, but the only work I can think of where it applies is the classic Duck Tales episode "Duck to the Future". Are there any others? (Flight of the Navigator doesn't count because that was time dilation, not time travel for the first "jump").