I've done a little reading, what there is to find, and it basically comes to the Telegraph declaring it to be so, but citing no source. Not even background, unnamed ones. It also bears pointing out that the Telegraph headline is damning to Nadal: "Nadal Makes a Mockery of Rule Book," implying that Rafa had something to do with Bernardes being withdrawn as a potential chair ump for his matches, which we don't even know to be true. So I would caution for a little closer attention to facts and sources before passing a lot of judgement.
The article does say that the ATP, which doesn't control majors, says that, “a number of factors are taken into consideration in the [umpire] selection process, including badge qualifications, nationality, as well as any previous history or incidentsâ€. The article also cites some precedents for the last part. I would think it possible, if it is true, that the ITF may choose not to pressure Nadal with an umpire that he has had a recent run-in with, especially at a tournament as important as Roland Garros.
Players can get frustrated in matches, and sometimes take it out on the chair. That's certainly not novel.
For the record, and @Carol35, I think Carlos Bernardes is an excellent umpire. One of the best, and most genial.