Hi benjykid - the object is somewhat ‘messed up’ already - look at the inside of the box by that hole - see how there’s a surface blocking the hole? Maybe that is what you are trying to fix? ExtractSrf and Delete this surface and the smaller one below, and do the same for all the holes along that edge. Then ExtractSrf the top and bottom faces of the top of thr box. Delete the hexagons for the holes you don’t want, then Untrim the trims in the top and bottom faces. You can then Join it all back up and Cap to close any planar openings.