In the past, I've kept them in separate catalogs named with a code that points or refers to the catalog that holds the transcoded media. We normally create main catalogs by "reel" or load ID.
AV1234R (for Raw)
Or anything like that will do it. Then you only search and use the catalogs that hold the transcoded media (the AV1234 for instance) and you can always know to just go to the R catalog to get the raw files.