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$ cat pm_1055846_name_id_data.txt
bananas 456
...
bana 20
bana-na 15
na 10

$ cat pm_1055846_name_replace_data.txt
bananas,oranges
...
bananas,oranges,pineapples,peaches,kiwis
bana-na,banana
ba-na-na,bana-bana,bana-nana

$ cat pm_1055846_name_replaced_out.txt
456,23
...
456,23,pineapples,897236,3726
15,25
ba-10-10,20-20,20-nana

my $re = '\b(' . join('|', keys %id_for) . ')\b';

my $re = '\b(' . join('|', sort { $b cmp $a } keys %id_for) . ')\b';

$ cat pm_1055846_name_replaced_out.txt
456,23
...
456,23,pineapples,897236,3726
15,25
ba-na-na,bana-bana,bana-nana

my $re = '\b(' . join('|', keys %id_for) . ')\b';

my $re = '(^|,)(' . join('|', sort { $b cmp $a } keys %id_for) . ')(?=
+,|$)';

s/$re/$id_for{$1}/g;

s/$re/$1$id_for{$2}/g;