I think this does what you want:

use warnings;
use strict;

my @charges = qw/ch1 ch2 ch3 ch4 ch5 ch6 ch7 ch8 ch1 ch2
                 ch3 ch4 ch5 ch1 ch2 ch6 ch7 ch4 ch3 ch9 ch2 ch4/;

my %bundle1 = map { $_ => 0 } qw(ch3 ch4 ch6);
my %b       = %bundle1;
my @final;
my @del;

for (@charges) {
    if (exists $bundle1{$_}) {
       delete $b{$_};
       if (!keys %b) {
          # seen them all, so reset
          %b = %bundle1;
          @del = ();
          push@final,'chx';
       } else {
          # keep it, in case not all are seen
          push@del,$_;
       }
    }
    else {
       push@final,$_;
    }
}
push@final,@del;  # add back any remainders
print "@final\n";
__OUTPUT__
ch1 ch2 ch5 chx ch7 ch8 ch1 ch2 ch5 ch1 ch2 chx ch7 ch9 ch2 ch4 ch3 ch
+4
[download]

One possible problem: it will slightly alter the order of your list if a partial bundle is seen.