Update to my question. I emailed Guedelon and the international press officer (Sarah Preston) responded to my question with the following:
Whilst I'm unaware of the existence of surviving templates or "moulds", there are a few medieval "tracing floors" on which designs for window tracery are preserved, for example at York Minster or Bourges Cathedral. These designs formed the patterns used to create wooden templates.
There is reference to these techniques being used in a number of texts and the financial records of medieval construction.
This lead me to look up more information thanks to the proper terminology (tracing floors). It would seem that the tracing floors are laid out on a plaster base and intricately carved/traced into the plaster at a scale and transferred onto larger stones.
From this, you can conclude that there were potentially shapeforms for the windows/arches at some point, if not constructed from a solid piece of stone. But these have been lost to time (Currently asking many medieval architecture professors if they have any knowledge of them existing) and Guedelon's use of shapeforms would be likely correct.
Below in the Flickr link is a set of modern window form recreations. Though I have done a bit of reading and at least have answered the main question, if any actual Medieval Architecture specialists can provide more information on the method of creating the tracing floors, or the construction of castles overall and your thoughts on the accuracy of Guedelon, that would be lovely.
Interesting quote regarding construction:
"It would have been easy to transfer a scaled floor plan constructed and measured using pins and string to the worker marking out the site with stakes and rope, without the need for modern aides." (J. Smith, Drawingmatter.org)
Citations/Links/further information for anyone more curious.
https://dokumen.tips/documents/the-working-space-of-the-medieval-master-mason-the-tracing-.html
http://papers.cumincad.org/data/works/att/ecaade2020_137.pdf
http://www.niallmclaughlin.com/wp-content/uploads/2014/10/The-Tracing-Floor.pdf
https://drawingmatter.org/medieval-masons-and-tracing-floors/
https://www.flickr.com/photos/11763518@N00/49846668838/in/photostream/