That's an interesting angle I hadn't thought of (I was thinking purely of toxicity).
I don't think it would make an appreciable difference, and if it did your body would probably recover relatively quickly (just as it does when you start eating meat again, though obviously it's a rough transition). I think the mechanism for supporting enzyme production is sufficiently separated from the presence of enzymes in your body that you would continue producing them, and the Beano would simply be supplementary. There are a LOT of complex carbs in your Soylent.
This site has a few quotes that should put you at ease. Regarding safety:
Supplemental enzymes perform very specific activities (amylase breaks down carbohydrates, lipase breaks down fats, protease breaks down protein). Unlike certain vitamins, minerals and herbs, there is no upper limit (or threshold) to the amount of supplemental enzymes that can be consumed. The reason for this is that the body has an estimated 100 trillion cells. Any one of those cells could be using thousands of different enzymes every second. This allows for huge quantities to be used by the body without overdosing.
And regarding the production of enzymes:
Supplemental enzymes support normal body organ function without replacing its effective working ability. We like to compare it to a raw food diet that is rich in enzymes. No one suggests eating raw food would inhibit the body’s natural production of digestive enzymes. The fact is the body will continue to manufacture the enzymes needed to benefit from food; supplemental digestive enzymes simply aid the digestive process.
EDIT: I should disclose that the site I linked offers enzymes for sale and has every incentive to provide misinformation. But it's information that corroborates my bias?