Will flipping the intake manifold affect the engine?

The manifold position is unimportant; its the carburetor you need to worry about. I assume we're talking about a 2 stroke here? There is a float in the carb that needs to be close to level. A little tilt one way or the other won't hurt, but too much and you'll run into either flooding or a lean condition, neither of which you want. A photo of the installed manifold and carburetor would help us answer you question more accurately. There might be other options open to you.
Tom