This is not quite correct. Where you deduct interest on your taxes is determined by what the money is used for, not what it’s secured against. So yes you probably can deduct the interest on the rental HELOC if you use it to payoff your primary, but it should be done under the home mortgage interest deduction, not on schedule E since you didn’t use the money to payoff or improve the rental.
I believe you can take deductions as long as it is for “buy, build, or substantially improve”, is for the same property that is securing HELOC and the same $750,000 limit.