If it was me, I'd make sure I had enough kegs to fill it. If I couldn't fill them all with beer, then I'd fill the rest with a Starsan solution. You could use plain water, but I would then add a small amount of bleach to keep the water fresh. This would add a lot of mass to the system and keep it from cycling too often. After a quick drain into another usable container, your keg(s) would be ready to fill with beer.
In any event, it's a good problem to have.