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jakemcree-
There's no harm in riding slower, taking longer breaks, etc. if you still finish the event.
Often I'd start a ride with a bit of knee pain and be worried and then after 30km I'd have forgotten about it and be smashing it by the end.
There's also no harm in making adjustments on the fly and judging their impact. Double check measurements beforehand and write stuff down so you can go back to baseline or note what works and then try that again next event.
hippy
You can do longer events in place of shorter events. They might even be good training if you're aiming for PBP. I don't see the point of qualifying with the bare minimum if you can do more and still be fit for the main event.
Depends on the nature of "knee niggle". I've ridden across the US with a knee niggle so they're not all super serious. I'd probably see a physio and look at what might have caused it, lower my gearing and then ride the planned events anyway - with a bail out plan in mind if the pain is too bad. That's what I did for Transiberica after fucking my knee up in TCR.
Going in to an event with an "I'm allowed to bail if this issue gets worse" mindset takes a lot of stress off.