Not sure if this really counts since it isn't "years later," but it's similar to the example from The Office above: in its final season, the TV series The Dead Zone relocated production from Vancouver to Toronto, and had to rebuild the standing sets of the main character's home. They modified them in subtle ways to incorporate improvements, but the modifications were subtle and the set was meant to look the same.
This also happened during the 3rd season of
7 Days when production moved from L.A. to Vancouver.
Professor Xavier's mansion in
X-Men was a historic building in Toronto. When the mansion reappeared in
X2, it was a set built in Vancouver. This was partially done to acommodate all of the action that takes place during Stryker's raid on the mansion in
X2. After all, you can't blow up a national landmark.
There were also 3 very different versions of the X-jet cockpit in the 3
X-Men movies. The thing underwent a total redesign between
X-Men &
X2. In
X-Men: The Last Stand, it was mostly the same except for a wall that now separates the cockpit from the midsection.
Then there are cases of real locations rebuilt or partially rebuilt on a stage or backlot, often screwing with the scale. They built their own versions of the head of the Statue of Liberty in both
Ghostbusters 2 and
X-Men. In both cases, the sets were larger than the actual head. New York City's famous Silvercup sign was recreated at a slightly smaller scale for the big fight scene at the end of
Highlander. (And then, portions of the Silvercup sign, the parking garage, & Connor McLeod's castle from
Highlander were recreated for Queen's "Princes of the Universe" music video.)