Come detto, non starei a complicarmi la vita così... Basterebbe una cosa del tipo:
codice:
Import System.IO
Import System.Collections.Generic

...

Dim fileName As String = ....
Dim out As New List<String>()
Using fs As New StreamReader(fileName)
    While True
        Dim r1 As String = fs.ReadLine()
        Dim r2 As String = fs.ReadLine()
        If r2 Is Nothing Then Exit While
        Dim s1() As String = r1.Split(";"c)
        Dim s2() As String = r2.Split(";"c)
        If CInt(s1(4))+CInt(s2(4)) < numeroMagico Then
            out.Add(r1)
            out.Add(r2)
        End If
    End While
End Using
Using sw As New StreamWriter(fileName)
    For Each s In out
        sw.WriteLine(s)
    End For
End Using