In fact it seems that Hoffman was lucky that these "Do Not Use" tapes had ever existed at all. According to engineer Bob Irwin (interviewed in Stereophile magazine, February 2002), in the mid-60s it was usual practice for the original mixdown tape to be used for disc-cutting, so the necessary EQ and compression would be applied at the mixing stage. This was apparently the case with Bringing It All Back Home and Blonde On Blonde; as a result, the original stereo tapes for these albums were worn out by the mid-80s, so the albums had to be remixed even for their first (1987) CD releases. With Highway 61 Revisited they just used one of the many cutting copies for the original CD.
Of course, the fact that the original "flat" stereo mix tapes for Highway 61 Revisited had been filed away marked "Do Not Use" meant that over the intervening years they had only been got out very occasionally for making a new cutting master tape. As a result they were in near-perfect condition, the only noticeable damage being a slight drop-out in the first verse of "Like A Rolling Stone".