The knives weren't ruined, but were prone to having knicks and making Korbanos Pasul (see Aruch Hashulchan Kodshim vol. 1, 18:17 that they would even do this to knives that they forecasted would eventually make Korbanos Pasul). Being that there was nothing physically wrong with them and people might keep using them to Shecht Korbanos, they were hidden away so that they would never be used. Alternatively, knives weren't that expensive anyway, so it wasn't worth the bother to melt them down and make a new one. A third possibility is that when we say that the other vessels were melted down, it doesn't mean they were totally melted down, but rather that they would come out of a light melting process looking like new (not like the hole in the vessel was just patched up). This would be difficult to do with a knife which has to be made in a precise way so that there are no knicks in the knife.

All the best,

Yaakov Montrose