I don't think that is really the OP's problem. What you suggest can be checked trivially by:

use strict;
use warnings;

my @array = (1 .. 8);

print "Before: @array\n";
nastyModifyParamsSub (@array);
print "After: @array\n";


sub nastyModifyParamsSub {
    for my $element (@_) {
        ++$element;
    }
}
[download]

Prints:

Before: 1 2 3 4 5 6 7 8
After: 2 3 4 5 6 7 8 9
[download]

Which shows that modifying the parameters is possible and that there is nothing magical about requiring $_ to do it. The following though shows one way that OP's code could be going awry:

use strict;
use warnings;

my @array = (1 .. 8);

print "Before: @array\n";
nastyModifyParamsSub (@array);
print "After: @array\n";


sub nastyModifyParamsSub {
    for (@_) {
        ++$_;
        clobberDefVar ();
    }
}


sub clobberDefVar {
    $_ = 0;
}
[download]

Prints:

Before: 1 2 3 4 5 6 7 8
After: 0 0 0 0 0 0 0 0
[download]

The bottom line though to that the OP's description is an fuzzy unclear thing and there is too much code and no data at all.