I have seen an article which cites a text called Massorah and this text supposedly catalogs 134 instances (referenced here) in which the written text "originally" used the 4 letter name of Hashem but the soferim changed the wording to be a-d-n-y. The article and its source material use the Masoretic notes as explained here.
I asked someone to take a look at the list and he worked with Sefer Yeshayahu in the Isaiah A Scroll while I looked at the Leningrad Codex.
While he feels that the number is inflated (he found that 4:4 in the Isaiah scroll already had a-d-n-y so no change is reflected) there are certainly situations in which he says that the Isaiah scroll has the 4 letter name but the codex has a-d-n-y.
The article I linked to suggests categories of situations in which soferim changed things but I don't know if that has any foundation.
Is there any Jewish source that discusses why there was a change in the cases where the codex has the word and the earlier scroll has the 4 letter name?