The reason %save_hash changes is because you are copy a referance to an array. If you print out $hash{$a} you will see it contains a referance to an array, and that is what you are putting into $save_hash{$a}. You need to work your way down to copying the values, one way to do this is below:
sub save_state
{
my %save_hash;
# foreach is your friend
foreach $key (keys (%main_hash)){
foreach $num1 (0..$#{$main_hash{$key}}){
foreach $num2 (0..$#{$main_hash{$key}[$num1]}){
# Now we are far enough down to copy the values
$save_hash{$key}[$num1][$num2] = $main_hash{$key}[$num1][$
+num2];
}
}
}
my @save_info;
push(@save_info,\%save_hash);
push(@save_info,\$aVar);
# etc. for all vars to save
push(@save_stack,\@save_info);
}
I sure that you will soon get a list of 1001 moduals that do this better.