Yes you need to include them. The IRS will want consistent accounting. If the properties that have a gain qualify for QBI, then the rental properties that have a loss reduce your rental gains that can qualify for the QBI deduction. Because you are determining that your rentals are a business venture, you are able to report expenses (and even have a reportable loss) through Schedule E. If, on the other hand, you were to determine that your rental is not a qualified trade or business, you are also stating it is not a for-profit activity and you would not be allowed to claim expenses or take a loss. And being able to claim the expenses on your return is more valuable from a tax standpoint than losing some QBI because you have to include the loss in your calculation.
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