I had LAX-SYD in F changed to DEN-LAX-SYD in F (AA-QF). In my activity statement, it shows up as a refund of the points used in the original booking, a change fee of 3500 and the points deducted from the new booking (different PNR and new ticket). Both 144k for the old and new. The taxes ended up slightly less, presumably due to transiting in LAX and not departing from LAX.
This is because origin-destination is still zone 8 for the new booking and priced at the rate of:
Qantas Classic Flight Reward table (worldwide) excluding taxes, fees and carrier charges
Points required for Classic Flight Rewards with Qantas, Airnorth, Fiji Airways, Air Vanuatu, American Airlines®, Emirates, Jetstar[SUP]~~[/SUP], QantasLink and US Airways[SUP]^^[/SUP].
See here:
https://www.qantas.com.au/fflyer/dyn/flying/using-points-awards-upgrades#classic-flight-rewards
Am I going to be up for cost of a whole new booking or will they recalculate the new itinerary as if it was one?
In the example above the QF website tells me:
SIN-DXB-JFK is 192k pts in F
BNE-SIN is 90k pts in F
BNE-SIN-DXB-JFK is 192k pts in F
Would I be up for a total of 282k or 192k if I added the BNE-SIN at a later point after making the original booking?
1. It will be the cost of a new booking. You get your original points refunded and get charged a 3500 point change fee.
2. 192k.
And if the point or origin wasn't being changed? If the example was the other direction adding on the SIN-BNE leg at a later stage?
It doesn't matter if the point of origin changes or not, a new booking is made (as above). Obviously these rules are different to those of other FF programs.
Depending on availability, if you travel on other partner airlines which requires a different (more expensive) points table, be prepared to be charged at a higher rate - I don't have experience with this, but don't say you weren't warned

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Ridiculous, isn't it - being charged different rates for different partners (even if part of OW)!