At least 3/4 of those 4000 lines is directly copied from Skype, and that's just one file. I don't think that's small enough to not matter; anyway, if it really was so small, it should easily have been rewritten with original code.

It's the size compared to the size of the relevant copyrighted work that matters, not compared to the size of the work it's copied into.

No that's a simplistic approach. Both matter, for example one volume of the Encyclopedia Britannica is a very small portion of the overall work, but it cannot be freely copied. Likewise if you write a book a million pages long, copying entire chapters does not suddenly become ok.

It is my understanding that "the relevant copyrighted work" in the Encyclopedia Britannica example is likely to be the article rather than the entire encyclopedia.

Is there the notion of minimum copyright infringement?

Yes and no. There is no such notion in copyright law. Case law is unclear, however: http://en.wikipedia.org/wiki/De_minimis#Copyright

The jury instructions issued by the judge in the ongoing Oracle vs Google case make considerable reference to the principle: http://www.groklaw.net/pdf3/OraGoogle-1018.pdf