I updated the script with the construction you suggested but the output was the same. I also noticed that there was an "I" missing from the sed statement and added it. Script: 
my $cmd = qq(ssh -qv $ssh_user\@$bkp_destination 'sed -i "s#.*$hostnam
+e#$skey#gI" /tmp/test.txt');
        warn "Launching [[$cmd]]";
        system($cmd) == 0  or die "Couldn't launch ssh connection via 
+[[$cmd]]: $? / $!";

[download]
Output: 
debug1: pledge: network
debug1: Sending environment.
debug1: Sending env LANG = en_GB.UTF-8
#ssh-rsa AAAAB3NzaC1yc2 root@HOSTA#g" /tmp/test.txt
debug1: client_input_channel_req: channel 0 rtype exit-status reply 0
debug1: client_input_channel_req: channel 0 rtype eow@openssh.com repl
+y 0
debug1: channel 0: free: client-session, nchannels 1
Transferred: sent 3312, received 2392 bytes, in 0.1 seconds
Bytes per second: sent 51671.7, received 37318.5
debug1: Exit status 0

[download]
From the $bkp_destination host: 
user@bkphost:/tmp$ cat test.txt
As123312123 asdasdadasqsef3w4rfweweweffwerfew
As123312123 asdasdadasqsef3w4rfweweweffwerfew
i12311231231231 HOSTA
As123312123 asdasdadasqsef3w4rfweweweffwerfew

user@bkphost:/tmp$ echo $h
HOSTA
user@bkphost:/tmp$ echo $k
ssh-rsa AAAAB3NzaC1yc2 root@HOSTA

user@bkphost:/tmp$ sed -i "s#.*$h#$k#gI" test.txt

user@bkphost:/tmp$ cat test.txt
As123312123 asdasdadasqsef3w4rfweweweffwerfew
As123312123 asdasdadasqsef3w4rfweweweffwerfew
ssh-rsa AAAAB3NzaC1yc2 root@HOSTA
As123312123 asdasdadasqsef3w4rfweweweffwerfew

[download]

In reply to Re^5: Send password in Net::SSH::Expect by gafaman
in thread Send password in Net::SSH::Expect by gafaman

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