Simply carrying out a flue gas analysis in this situation will tell you nothing ,unless a serious return of Products, in which case other faults would have shown long before testing was required, an analysis of the air intake MAY have shown if the joint seal had failed but I have seen flue O rings fouled without any cross contamination of products but condensate can still drip, OP your engineer has called it correct so far so let him do his job
So the flue gas test is to see if any flue gases have leaked into the air intake? I presume a co/co2 leak into the intake would then be measurable in what ends up coming out of the flue.
The fold in the seal was very small. I can see that water would leak past but i would expect that the actual gap left by the fold would be tiny.
So there is no definitive test for the integrity of the flue seals? The reason for all the questions is the boiler is in my son's playroom and directly underneath his bedroom.