Saving a map will always resave the map's BuiltData, even if the BuiltData hasn't been marked dirty. Changes were made to avoid marking it dirty for [Link Removed], but the call to SaveWorld in FEditorFileUtils::SaveLevel ignores the dirty flag and tries to save it anyway.
In 4.27, marking the map as Writeable and saving it resulted in a prompt to check out the BuiltData file. In 5.0, the second prompt did not appear and the save failed because the BuiltData was not writeable.
There's no existing public thread on this issue, so head over to AnswerHub just mention UE-119080 in the post.