print OUT if ((s/m/$uut_names[$i]/) && (s/in1/$nets[$i]/) && (s/output/$enabled_nets[$i]/));

there is no output being written to file here

You are missing the while (<IN>) { ... } loop around this statement. print defaults to writing $_ when called without arguments or only a file handle.

Stupid demo:

>perl -E "open IN,'<','/etc/group'; open OUT,'>','/tmp/foo'; while (<I
+N>) { print OUT if /adm/; } close OUT; close IN;"
>cat /tmp/foo
sys:x:3:root,bin,adm
adm:x:4:root,adm,daemon
disk:x:6:root,adm
>
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Alexander