Your problem seems similar to one answered by tachyon in Re: Formatting questions. His example code slurps in all the lines from the file at once and then splits on the leading pattern, something like this:

use strict;
undef $/;
my $data = <>;
my @data = split 'checking', $data;
shift @data;
my @bad_files;
for my $bit (@data) {
   my ($file_name) = $bit =~ /file <([^>]+)>/;
   push @bad_files, $file_name
      if ($bit =~ /media does not exist/);
}
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