Could not understand properly. Here is your code, with just print statements commented. I am getting correct output for all enteries, for all lines. 
use strict;
use warnings;

my @input = (
    "Figure <xref ref-type=\"fig\" rid=\"F1\">1</xref> Figure <xref re
+f-type=\"fig\" rid=\"F1\">1</xref>",
    "Figure <xref ref-type=\"fig\" rid=\"F2\">2</xref>",
    "Figure <xref ref-type=\"fig\" rid=\"F3\">3</xref>"
);
my $isize = scalar(@input);
my ($same , $dx1 , $dx2);
for (my $il = 0; $il < $isize; $il++ ) {
    $input[$il] =~ s/<xref ref-type="fig" rid=/\\protect\\customizeref
+{/g;
    if ( $input[$il] =~ /\\protect\\customizeref{(.*?)<\/xref>/ ) {

        # $input[$il] =~ /<xref ref-type=" fig " rid=" ( . *? ) < \/xr
+ef>/;
        #print("$1\n");
        $_    = $1;
        $same = $1;
        $dx1  = /"(.*)"/;
        $dx1  = $1;
        $dx2  = />(.*)/;
        $dx2  = $1;
        #print("$dx1\n");
        #print("$dx2\n");
        $input[$il] =~
        s/\\protect\\customizeref{$same<\/xref>/\\protect\\customizere
+f{$dx1}{Figures}{}/g;
        $input[$il] =~ s/$same/$dx1}{Figures}{}/g;
}

if ( ( defined $same ) and ( defined $dx1 ) ) {
    #print(">$same\n");
    $input[$il] =~ s/$same<\/xref>/$dx1}{Figures}{}/g;
}
print $input[$il], "\n";
}

[download]
Here is the output. Let me know if it is correct. 
Figure \protect\customizeref{F1}{Figures}{} Figure \protect\customizer
+ef{F1}{Figures}{}
Figure \protect\customizeref{F2}{Figures}{}
Figure \protect\customizeref{F3}{Figures}{}

[download]

In reply to Re: Multi replace in a Line by gurpreetsingh13
in thread Multi replace in a Line by veera

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