My (limited) understanding of prototypes is that they modify the way perl parses your code.

Which means that

sub foo($) { ... }

bar foo $arg1, $arg2
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parses as bar(foo($arg1), $arg2) Whereas without protoypes it parses as bar(foo($arg1, $arg2))

So you could break things by just removing prototypes.

Update: A code example to test this:

sub foo($) {
    print "foo: $_\n" for @_;
    return "returned from foo";
}

sub bar {
    print "bar: $_\n" for @_;
}

bar foo 1, 2;
__END__
# with prototype on foo:
foo: 1
bar: returned from foo
bar: 2
# without prototype:
foo: 1
foo: 2
bar: returned from foo
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Another way to test this is using B::Deparse: perl -MO=Deparse -e 'sub f($) { 1 }; sub bar { 2 }; bar f 1, 2'