Thank you very much! This explains everything. So I tried with this code :

open O, ">a.bin";
binmode O;
print O "Hello World!";
close O;

link "a.bin", "b.bin";

open L, ">b.bin";
binmode L;
print L "Bye World!";
close L;

open O, "a.bin";
print while ( <O> );
close O;

# prints "Bye World!"
[download]

This proved an in-place edit works in binary files as expected. It's glad to know that it's my fault!! Otherwise I don't know how to fix it. Good day! =)