For a situation like this, I'd probably try the "IN (...)" expression in SQL. I haven't tried DBIx::Abstract, so here's what I would do with straight DBI calls to create, prepare and execute the a suitable SQL statement, using placeholders for the array values:

my $sql = "update table set Y=0 where X in (" .
            join( ',', map { '?' } @ARRAY ) .
            ")";

my $sth = $dbh->prepare( $sql );

$sth->execute( @ARRAY );
[download]

I'm clueless as to whether DBIx::Abstract provides a means for doing this sort of statement construction. If not, that's sad, but you should just be able to fall back on straight DBI calls whenever you want/need them.