I think I lost a bunch of Kontakt multi-rack stuff in multiple projects once, when I reloaded Windows, and I still have scar tissue.
Since then, anytime I tweak presets in any synth, I always save that new/altered preset to a sub-folder within my Cakewalk Project folder, or to a User-Preset type folder for whatever synth it is for (most have somewhere they use for saving and loading of user-defined presets).
I think one of those user-built Sonar utilities performs some sort of building of an inventory list of everything used in a project, but I do not know if it saves off preset info.
In addition, I am not sure if any Sonar awareness of plugin settings would be maintained across a Windows reload, though I am hoping folks chime in with ways of your accomplishing the saving of such info prior to your reload.
Bob Bone