In short, yes the Nanocom will be able to resync a different engine ECU to the BECM.
However, as Sloth says you would also need to change the BECM setting from Auto to Manual, and a load of looms etc would need to be swapped too, to allow for the manual box and clutch pedal etc.
But as far as the diagnostic side of things - yes, a Nanocom will do all that.
'06 4.2 Supercharged Black/Cream "Jess" -- Bought April 2021 (NZ)
'01 4.6 Vogue Black/Lightstone "Snog" -- Bought Jan 2012
'99 4.6 HSE Cobar Blue/Lightstone -- Sold March 2009
'95 4.6 HSE Epsom Green/Tan -- Traded June 2008