From Google:

Activated carbon air filters consist of a vast system of pores of molecular size. These pores are highly adsorbent, forming a strong chemical bond/attraction to odorous, gaseous, and liquid contaminates, especially organic chemicals/compounds. Vast surface area enables these carbon filters to adsorb exponentially more contaminants and allergens than traditional carbon. Adsorption is a distinct process where organic compounds in the air or water react chemically with the activated carbon, which causes them to stick to the filter

They are essentially supposed to filter better.

If I'm not mistaken, all of the vents pull air from the cabin air filter. So a blockage on the filter shouldn't result in just one or two vents flowing low. This would lead me to believe that replacing the filter wont impact your problem at all. I would say you have some other issue like the "flaps" that you previously stated.

If it makes you feel any better. My X also blows stronger on the passenger side. If yours is configured the same way, the cabin air filter is on the passenger side a very short distance away from the passenger vent. I think the difference in distance and the way the vents are designed/routed may have something to do with this. There may not be any actual problem. It may just be a result from the design.

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2007 E70 X5 4.8i Sport Package
8x,xxx Miles
"My Precious" (Smeagol voice)