Try this

my %aff;
while($str=~/<affiliation id="([^"]*)"><label>(.+?)<\/label>/sgi){
$aff{$1}=$2;
}

for my $affid (sort keys %aff){
$str=~s#(<crossRef refid=")(">\Q$aff{$affid}\E</crossRef>)#$1$affid$2#
+sgi;        
}
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