If the situation is that these things are sequential as in your example data, this is a common pattern that does not require the storage of the output array.

#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;

my $line = <DATA>;  #get started with first line
chomp $line;
my ($prev_sidpart,$prev_rest) = split /\|/, $line;

while (my $line = <DATA>)
{
    chomp $line;
    my ($cur_sidpart,$cur_rest) = split /\|/, $line;
    if ($prev_sidpart eq $cur_sidpart)
    {
        $prev_rest .= " $cur_rest";
    }
    else
    {
        print "$prev_sidpart|$prev_rest\n";
        ($prev_sidpart,$prev_rest) = ($cur_sidpart,$cur_rest);
    }
}
print "$prev_sidpart|$prev_rest\n"; #last record

=prints:
sid  1|FLPSDFFPS LLWFHISCL WIRTPPAYR YVNVNMGLK
sid  2|FLPSDFFPS LLWFHISCL FLPSDFFPS ELMNLATWV
sid  7|FLPSDFFPS ATVELLSFL VWIRTPPAY LLSFLPSDF
sid  9|VWIRTPPAY LLDTASALY FGRETVLEY PSDFFPSVR
=cut


__DATA__
sid  1|FLPSDFFPS LLWFHISCL
sid  1|WIRTPPAYR YVNVNMGLK
sid  2|FLPSDFFPS LLWFHISCL
sid  2|FLPSDFFPS ELMNLATWV
sid  7|FLPSDFFPS ATVELLSFL
sid  7|VWIRTPPAY LLSFLPSDF
sid  9|VWIRTPPAY LLDTASALY
sid  9|FGRETVLEY PSDFFPSVR
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