I can see two problems with your system command: (1) parts of your hashed password strings contain $ signs which will be interpreted by the shell as environment variables. (2) If you then single quote your s/// expression to protect from shell interpolation, those same $ signs are interpreted as variables by Perl; the slashes are also interpreted by Perl. So replace this:
system("ssh -o StrictHostKeyChecking=no root\@localhost /usr/bin/perl
+-p -i -e s/$hash2/$hash1/ee ha
+shfile")
with this:
system("ssh -o StrictHostKeyChecking=no root\@localhost /usr/bin/perl
+-p -i -e 's/\Q$hash2\E/\Q$hash1\E/' ha
+shfile")
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