You should simplify your code to only open the counter once. Otherwise you have a race condition.

open FH, "+< counter.dat" or die $!;
flock(FH, 2);
$id = <FH>;
$id++;
seek(FH, 0, 0);
truncate(FH, 0);
print FH $id or die $!;
close FH or die $!;
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It would be more elegant to use a database with an autoincrementing key.

After Compline,
Zaxo