oops, you are right, I had supposed that the strings didn't overlap...

but if the substrings are sorted by their position on the original string, it's easy to solve, just make $after=$pos+1 or:

my $pos=0;
foreach my $sbstr ( @$array ) {
       $pos = index $str, $sbstr, $pos;
       substr ($nstring, $pos, length ($sbstr)) = $sbstr;
       $pos++
}
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and if they are not sorted, well, then you can use some hash to remember the last $pos for a given $sbstr and start searching after that...

my %after;
foreach my $sbstr ( @$array ) {
       my $pos = index $str, $sbstr, $after{$sbstr}||0;
       substr ($nstring, $pos, length ($sbstr)) = $sbstr;
       $after{$sbstr}=$pos+1;
}
[download]