Changing plurality in parentheses

If a set of parentheses lies between a subject and its verb, and the parentheses contain an substitutive subject whose singularity/plurality disagrees with the original subject, whose singularity/plurality should be chosen for the verb?

In other words, in the following example, should "questions" (and its verb "are") be singular, or should they remain plural as shown?

Many (if not every) questions on this StackExchange are answered.

My intuition tells me that the two words in question should remain in plural forms, since the text in parentheses only interrupts the sentence (and the sentence would be grammatically incorrect if everything in parentheses were removed and the words were in singular form). On the other hand, when read aloud (assuming one reads the text in parentheses), this has an uncomfortable sound to it, and I've seen others write in what would be the above example's singular-form case, so I'm curious to find out which is correct.

And, thinking about it, I suppose the same question would apply when commas are used in place of parentheses.

The "uncomfortable sound" of the example is due to the clash, or lack of parallelism, of "many questions are" with (in effect) "not every question is". The problem can't be fixed just by substituting something for "questions" and something for "are"; instead, rewrites along the following lines are needed:

Many questions (if not every question) ... are answered.
Many (if not all) questions ... are answered.
All but a small number of questions ... are answered.

All of these are correct forms. The first one still has a difference in number between the main subject and the parenthesized one, but with parallelism more properly established than in the original sentence, that problem of style is less glaring. The second form is quite similar to your original, with all in place of every.

Parentheses are usually used for additive phrases / clauses which give additional information. They neither affect the number of the subject of the main sentence, nor the number of the verb.