I just ran the live update again and it did the same thing. I had the YVR folder open at the same time and watched it disappear after I said that I don't want it replaced.
I can only repeat and confirm it doesn't do that. In fact, I made additional safety checks in this update, but the file wasn't removed in the previous version as well.
However, if you *name* your custom AFCAD using a different name than the FSDT one, it WILL be deleted in any case so, if you want to keep it and not being overwritten, it must have the same name as the one that comes originally with the scenery.
This is important because, if you change the name, the GSX customization we supply for our sceneries won't be loaded, so everything will work "as default" and, in case of CYVR and any scenery we did GSX/SODE jetways, this will lose all jetways.