Some thoughts .. (you have identified the main concerns in your post) -
First consideration is procedural -
(a) is the swap permitted by State of Registry and local regulatory requirements as well as operator requirements ?
then the technical considerations -
(b) do the two aircraft have the same loadsheet/trimsheet specified. That is to say, the AFM/POH/W&B manual data and configuration must apply equally for one as well as the other.
(c) if (a) and (b) are OK then, providing the empty weight and CG (moment/IU) data are corrected for the hull change, all should be fine.
However, from a practical point of view, for a sensible trimsheet system, the loadsheet could be reworked for the aircraft swap in a minute or so. Is going to the trouble you propose worth the effort ? A competent tech crew member could do the work in the cockpit with little time loss.