The printer have 3 vacuum zones only, each of them consists of a bar of multiple fans. You will run into much bigger problems as just leading edges of thin media fluttering in the wind if one of them blows (media will not feed directly into or out of the printer for example). Have someome replaced components of your vacuum system shortly?
Howsoever, the vacuum sucks through every hole of the belt, the covered and the uncovered ones ... this could lead to an airflow in the printer what could lead to fluttering leading edges of thin media. If this is a problem, I would suggest to print roll-to-roll (as the manual does too).