Well.......
If it's a 720 GTI... and the single is good to go... then do the swap. Seadoo listed the 720 as the same power and RPM with either the twin 38's, or a single 40. When my shop was open... I worked on both, and I never noticed a performance different. (other than being in different skis) To be 100% honest, I'm not sure why they did both.
The only down side that I can think of... is on some really hot skis, we ran the rear cyl a little rich because of crank twist (it runs hotter) SO... if you richen it to keep the rear happy... the front may foul or load up on long idles.
Anyway... since you will be changing him labor... I'm sure it would be WAY cheaper for your customer to just do the swap. Especially if the rubber gaskets are still good. It will only be 2 hr's labor for the swap opposed to 3 or 4 hr's, plus any parts needed for the rebuild.