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#!/usr/bin/env perl

...
    s/$re/$id_for{$1}/g;
    print $out_replaced_fh $_;
}

$ cat pm_1055846_name_id_data.txt
bananas 456
oranges 23
peaches 897236
kiwis 3726

$ cat pm_1055846_name_replace_data.txt
bananas,oranges
...
oranges
kiwis,oranges,bananas,bananas
bananas,oranges,pineapples,peaches,kiwis

$ cat pm_1055846_name_replaced_out.txt
456,23
...
23
3726,23,456,456
456,23,pineapples,897236,3726