FAQs #1

Surely there's so much evidence against Gilles de Rais that his guilt is beyond doubt?

Not at all. In fact, the first hint that he may have been unjustly condemned came in January 1443, when the King made a gesture towards acquitting him. Although most of the writers who produced sensationalised versions of his life over the centuries had no interest in questioning the orthodox narrative, there have always been dissenters. In the twentieth century the trial record became easily available, first in 1921 (in a version produced by Fernand Fleuret) and then in 1965 (in Pierre Klossowski's translation). It is no coincidence that these dates marked sudden upswings in revisionist thought. Once it was possible to buy and read a modern French translation of the trial, it became abundantly clear that considerable chicanery took place. Even traditionalist writers were forced to accept that it is undeniable that there was a plot to bring about Gilles' downfall. Their case now rested on the notion that the Duke and the Bishop had conspired against a man who was a dreadful villain, and just happened to own the estates that the Duchy had coveted since before he was born. The many discrepancies and contradictions in the evidence, which had been ignored by biographers, were now exposed, although few bothered to look for them. All existing biographies contain monstrous errors and promulgate non-historical myths such as the veiling of the cross and the illustrated Suetonius.

Further reading:
An Overview:The Truth About Gilles de Rais

The Veiling of the Cross

But what about the bones that were found in some of his castles? 

There were no bones. At several points during the trial, there are claims about human remains – mass cremations at Machecoul, a conduit full of children's bones at Champtocé, a couple of skeletons found at Machecoul. These, however, are unsupported allegations; no forensic evidence was produced in court. In more recent times, there have been several rumours of bones found at one or other of Gilles de Rais' castles, but these always prove to be just that – rumours. The most recent was supposedly located at  La Suze-sur-Sarthe, which was not even part of Gilles' estates.

Further reading: 
Dem bones, dem bones, dem dry bones...
The Beast of Extermination: a numbers game