The best quality manuscript of the Paippalada recension of the Atharva Veda was discovered only in 1957. I believe there is a large number of palm-leaf manuscripts that have not yet been scanned and digitized. There must be other manuscripts in existence not known yet.
Major scriptures like the Itihasas and Puranas exist in multiple versions and bodies like BORI have prepared Critical Editions of some of them to filter out interpolations and incorporate all the known original materials.
Is any religious/government body working on preserving these manuscripts before they get lost?