Assuming your values are one string of space delimited words, rather than an array(ref).

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

my @tocheck = qw/Apple Corn Pie Fish/;
my %checkfrom = (
    Meat  => 'Fish Apple Pork Bacon',
    Fruit => 'Apple Pie Orange Beef'
);

my $ra = Regexp::Assemble->new;
$ra->add( @tocheck );

for (values %checkfrom) {
    s/$ra//g;
    $_ = join ' ', split; # delete spurious spaces
}

say dump(\%checkfrom);
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