Tempest 2000 -- people probably forget now because it was on Jaguar, but this game revived a completely dead classic arcade IP to huge acclaim.
Wolfenstein 3-D -- while not officially licensed (I don't think) this was meant as a reboot of the classic Castle Wolfenstein and became so much more. Notably Return to Castle Wolfenstein, and Wolfenstein: The New Order were both excellent reboots as well, so this series seems a bit blessed in this regard.
Fallout 3 -- Still a controversial change of direction but took a cult classic and made it into one of the biggest successes of its time.
Deus Ex: Human Revolution -- One of the very few games that managed to crack the code and make an accessible, commercially successful immersive sim that was still great.
Prince of Persia Sands of Time -- Again plucking a franchise that no one saw any value left in and creating a massive hit, that Ubisoft coasted on to diminishing returns for many years.
Doom (2016) -- Instead of rehashing an old game or hammering an old game into modern tropes, id really thought about how to make this game work for modern audiences without losing what it is and came up with something really unique.
God of War (2018) -- Took one of the most dumb/macho action games and turned it into a brilliant examination of fatherhood and masculinity. I still cant get over how unexpected and brilliant it is.
Spec Ops: The Line -- Totally subversive. Took a dumpster tier series and used it as a platform to really challenge the kinds of stories the genre and medium can tell.
I don't really count this. It wasn't a conscious effort to reboot the series so much as duct taping a trademark that would have lapsed onto an unrelated game for the purposes of IP squatting.