Read file line by line and write lines you need to another file. Once finished replace old file with new.

Here some code which looks a bit cryptic but check this node, perldoc perlrun and perldoc perlvar and it should be become clear.

{
   local $^I = '';
   local @ARGV = ($filename);
   while (<>) {
       next if CRITERIA_TO_SKIP_LINE;
       print;
   }
}
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