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The cathedral in Cologne was extensively damages during WW2 and I suspect many churches in Germany, and indeed throughout Europe, had to rebuilt as well. Might be worth a look at the debates that took place then.
They don't seem very modified, at least not to 1950-1960s architecture, so not sure that the modernists have much of a point.
Also, redoing part of say a 13th century church in the 16th century, in 16c style, will have been less of a clash than using modern architecture now. Building materials, if not necessarily building techniques, just didn't change that quickly back then.
I smell a distinct potential for Colonnes de Buren here.
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The restoration of the Sistine Chapel comes to mind. It was done in the 1980s and 1990s.
Before the restoration, everyone was used to the dark colors. There was 400 years of accumulated gunk on them, but they were "the way it was supposed to be".
When the restoration was complete, many traditionalists howled at all the bright colors (even though the colors would supposedly be closer to the original).
No matter what you do, you are going to seriously offend a group of people.