In case it is useful for someone, I've written a perl routine to solve this problem.

sub create_header {
my $p_input_bams = $_[0];
my $header_file  = $_[1];
my $RG_string = "";
my %rgs;
foreach my $b ( @{$p_input_bams} ) {
    open(J,"samtools view -H $b|") || die "cñakjdñakj $b\n";
    while(<J>) {
        #print STDERR "$_";
        last unless(/^\@/);
        if(/^\@RG/) {
            $_ =~ s/\#[0-9]+//;
            $rgs{$_} = 1;
        }
    }
    close(J);
}
foreach my $rg ( keys %rgs ) {
    $RG_string .= $rg;
}
print STDERR "RG_string=\n$RG_string\n";
my $main_bam = $p_input_bams->[0];
open(IB, "samtools view -h $main_bam |") || die "Cannot open main: $main_bam\n";
open(OB, ">$header_file") || die "cannot write to header: $header_file\n";
while(<IB>) {
    last unless(/^\@/);
    if(!/^\@RG/) {
        print OB;
    } else {
        print STDERR "Printing RG string...\n";
        print OB $RG_string;
    }

}
close(OB);
close(IB);

}

To use it:

system("samtools merge -cf $lib.merge-changeHeader.bam @input_bams");
&create_header(\@input_bams,$header_file);
system("samtools reheader $header_file $lib.merge-changeHeader.bam > $lib.merge.bam");