;read files and put into arrays
$file1=Readfile(File1)
$file2=Readfile(File2)

;loop through files removing matches
for $i=0 to ubound($file2)
  for each $line in $file1
    $index=ascan($file2,$line)
    if $index>-1
      $file2[$index]=""
    endif  
  next
next

;build new arrary based on file2
for each $line in $file2
  if $line<>""
    redim preserve $output[$j]
    $output[$j]=$line
    $j=$j+1
  endif  
next

;use $output array to display your records, or create/overwrite a file

; variables should be declared!
$aFData1 = FileIO($Source1, 'R') ; read the first (Master) file
$aFData2 = FileIO($Source2, 'R') ; read the second file

; Convert the master file to a delimited string to simplify matching the second file array
; The source will look like "~line1~line2~line3~...~"
; The delimiter character chosen MUST NOT appear in the source data. Use "Chr(3)"
; as a non-text delimiter if this is an issue (replace "'~'" with "Chr(3)" in this example)
$Source = '~' + Join($aFData1, '~')

; Enumerate the file to "clean up" - lines that exist in file 1 will be removed
For $P = 0 to UBound($aFData2)
  ; If the current line "~line#~" is found in $Source, clear it!
  If InStr($Source, '~' + $aFData2[$P] + '~')
    $aFData2[$P] = ''
  EndIf
Next

; All dups have been removed from the second file - write it back, trimming blank lines
$aFData2 = FileIO($Source2, 'W', 2)