It'll run well enough, although I'm not sure if the map will have enough adjustment in its settings to deal with the smaller cylinder capacity.
In theory it bases fuel injection timings on the amount of air going in, throttle position, along with fuel and engine temperature, opening the injectors long enough to deliver the appropriate amount of fuel required to maintain the optimum stoichiometric ratio.
Wether or not it's sensitive enough to work out its running a 3.5 or a 3.9 I couldn't tell, although the lambda sensors will help give it a bit more of a clue as to if it's over fuelling or not.
My old boss once had an argument with me on a similar subject when we replaced a 1.4 K Series in a Rover 25 with a 1.8 lump, he was adamant that the ECU would compensate for the extra capacity.
The response that he'd been doing the job 30 years so he should know when asked why the ECU's were different part numbers if things were the same didn't really cut it with me.
As mentioned, it's worth taking the opportunity to have a chat with Mark Adams. I'm fairly clued up, he is THE authority.