Two suggestions -- one is to restructure the hash search and replace a little for less iterations, and the other is to split on "WARNING" instead of just matching, so you can work on the pieces separately.

my $keysForRE = join '|', keys %date_hash;
while(<FILE>){
    s/\b($keysForRE)\b/$date_hash{$1}/eg;
    my ($piece1, $piece2) = split /\bWARNING\b/, $_, 2;
    # do stuff to $piece1
    # do stuff to $piece2
    $_ = join 'WARNING', ($piece1, $piece2);
}
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