Ok so we have more than 2 not to current standards (which no longer exist) so we can raise the classification to AR. If not to current no longer exists where do we stand ?
As the above said we can only class as AR if combustion is being affected. The top flue is natural draught and probably has no test point to examine emmissions and unless you get up a ladder to test it we won't know either way.
Heat rises and it is extremely unlikely that it would go down and be pulled into flue 1 (possibly, maybe, one day, if...)
Yes it is too close to the extractor which we assume blows out, but it could, possibly, maybe one day, if... re-enter through the ducting.
It is also too close to the external corner should be 600mm for natural draught.
Flue 1 is fan draught and will be pushing fumes away from the building, but again possibly, could, maybe, one day, if... cause flue 2 to draw its products into its air intake causing incomplete combustion due to already burnt oxygen being used as its air supply.
We are using a lot of if's and maybe's in this conjecture and even if we say it is AR we cannot make you turn it off, we are only advising you.
If I know something is only AR due to paperwork I'll let the cust know I'm just covering my backside, if I think it poses a slightly more higher risk I'll let you know that I wouldn't let my mum use it, however I'm too honest and not touting for work in this instance.
Again there are thousand upon thousand of scenarios like this throughout the country.
Eg bend on flue before 600mm, wrong terminal and height above roof pitch, doesn't mean I'd turn your boiler off if it meets all my safety checks.