Not sure I understand the question, but I think the answer is No.
It's true that modifying the movement will wreak havoc with the balance,
so some pairs may be compared more or fewer times than they should.
But the edited movement represents what was actually played, so that's
what you should do.
I suppose you could switch up other tables in later rounds to try to
restore the balance, but it's subject to great potential for error, and
I don't think it's worth the effort.
Besides, a lot of Howell movements are unbalanced to start with....