Any particular reason it be to be in a single string? an array would be much easier to process and involve less character handling while doing the replacements.

use strict; use warnings; use feature 'say';
my @lines=<DATA>; 
for my $line (@lines) {
    chomp $line;
    if (index($line, 'SUBSTR') > -1 ) {$line='FOO'; } 
}

#for my $line (@lines) {  say $line; }

my $fileContent=join("\n",@lines); 
say $fileContent; 

__DATA__
path/to/some/file
path/to/some/other/file
path/to/SUBSTR/file #replace entire line if SUBSTRING is found
path/to/file
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