I did it so:

use Modern::Perl;
use Data::Dump qw/dump/;

my %acn_database;
while (<DATA>) {
    last if /END/;
    my ($acn, $orfname) = split /\sORFNames=|\s/;
    $acn_database{$acn} = [$orfname];
}
while (<DATA>) {
    my ($acn, @pf_data) = split /\s\|\s|\s/;
    push @{$acn_database{$acn}}, @pf_data;
}
say dump(\%acn_database);


__DATA__
Q197F8 ORFNames=IIV3-002R
Q197F7 ORFNames=IIV3-003L
Q6GZX2 ORFNames=FV3-003R
Q6GZX1 ORFNames=FV3-004R
Q197F5 ORFNames=IIV3-005L
Q6GZX0 ORFNames=FV3-005R ;PF02393
Q91G88 ORFNames=IIV6-006L ;PF12299;PF04383
Q6GZW9 ORFNames=FV3-006R
END
Q197F8 | PF04947.9
Q91G88 | PF01486.12 PF00319.13
[download]

I have assumed that the stray space at the first line of your first file is just a typo.

Note that this will still do the right thing if you have multiple lines in your second file with the same accession numbers: their data will just be added to right array in the hash.