The Taharas ha'Kodesh actually changes the Girsa in Rashi due to your question. However, Rashi earlier (on 40a) also writes that the entire vat will be disqualified. The Olas Shlomo answers according to the Ran in Nedarim (52a) that only Isur is Batel in Heter, and the dye -- although it will not dye the Tzizis properly -- is not considered Isur.

In a similar vein, there are those who prove from the Rosh in Chulin that Bitul can only take away negative characteristics, such as Isur, but it cannot give the substance which became Batel any positive characteristics. Although this rule does not seem to be universally accepted, it may apply here.

D. Zupnik