Hi kyounger,
Hmmm...
Definitely an odd symptom. Because, as you say, it starts right back up.
Is this remote or tiller? If tiller, pull only or electric start?
Does the fuel line bulb remain firm when this happens? Like Milgrip says, it could be something with the fuel supply line or pickup or maybe even the fuel tank vent.
Have you ever removed and drained the fuel chamber? Item 2 in the link below:
https://www.boats.net/catalog/honda/...9999/fuel-pump
The fuel chamber collects water over time and should be removed and drained of all liquid periodically to prevent it causing problems.
If you can't find a fuel supply cause for this then, as racerone suggests, you will need to find out if it's losing spark during the occurance. Even with a timing light hooked up it might be hard to catch though.
When was the last time you replaced the spark plugs? Sometimes a new set of NGK CR5EH-9 plugs can work wonders. I have a 2006 BF 20 D and have not experienced these symptoms..
Get back to us about what you're finding and we will keep trying to think of things to try.
Good luck.