Line 118 is

if ($temp[4] ne '=0'){
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so obviously $temp[4] is not set. You set it depending on

if ($_ =~ /^(\@pRECTYPE=\"SBSB\")(.*)(\@pWMDS_SEQ_NO)(1)(=\d{1})(.*)(\
+@pWMDS_SEQ_NO)(2)(=\d{1})(.*) .....
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in line 95. So you should investigate why the regex is no longer matching. Probably some encoding issue between the Linux and Windows version of <UPDFILE>...

HTH, Rata