I see now where you're aiming at. You mean "Pelasgian" as a (non-IE, presumably?) substrate in Greek? Well, let me say this, one crucial question here: are these words in modern Greek? Are they attested in Classical Greek or in Mycnenean Greek (if they are an ancient substrate, they without a doubt are attested)? Because, if yes, they would be obviously subject to sound changes.
The most over sound change from classical to modern Greek is the treatment of φ, θ and χ. In classical Greek, these were aspirated p, t and k, respectively (hence transliteration as ph, th and kh). However, in modern Greek, they changed to f, th (like English "thunder") and ch (as in Scottish "loch"). My point here is: any borrowings from a substrate language would be subject to such sound changes, too, and would give us a different image of this language.