Yes, here are the steps you'll take:
Create the race on the main finish line computer. Set the number of "Laps" equal to the total number of times Arrow needs to accept. For example if you're timing a 10K and they want only a 5K split. Then set the number of laps to 2 and name each split in the "Split Descriptions" tab BEFORE you push the race to Arrow. Basically we're just letting Arrow know how many splits it needs to capture and what to name each split.
After you push the race (and split descriptions) to Arrow, you can now set each PC up to track only the number of splits that particular PC needs to track. So in this example you'll set up the finish line PC and the 5K split PC up to track just 1 lap in ART.
Both computers will need to be online of course. As they come through the 5K split, those times are pushed up to Arrow as their first split, then of course the 2nd time sent to arrow is their finish time.
If someone is missed at the 5K split, then of course their finish time will appear as their 5K split on Arrow, but the official results coming from ART will of course have everything correct.
When you import the 5K splits into the finish line computer (which I'd do when you're home after the race), then you can resync with Arrow if you want.