Oh right you shouldn't be in there without the right test equipment especially if you don't know what you're doing. That's inside the combustion flue system.
That's the automatic air vent and should be loosened all the time. They have a habit of getting muck in and leaking though.
You probably dislodged the programmer cable in the process of opening the case and moving the circuitry down, as the cable might have snagged.
As above, you shouldn't be removing the casing of the boiler unless you're Gas Safe Registered, as it forms the safety room seal and the 26:9 checks need to be carried out by a competent engineer before the boiler is used again.
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