Created materials are stored in %APPDATA%\Allegorithmic\Substance Alchemist\CreatedMaterials.
You should probably back up file %APPDATA%\Allegorithmic\Substance Alchemist\alchemistDatabase.json as well, it contains all the references to all materials alchemists know. Trying to import an alchemist tree material (.json files) can be troublesome.
But it's probably simpler to export the project (file -> export project), wipe out your data %APPDATA%\Allegorithmic\Substance Alchemist, and reimport the project.