I would think that you would be better off adding isomerized extract. However, consider this:
Boiling in water will probably not create the bitter acids as it would in wort, which is more acidic. Maybe acidifying the water a bit first would be worth a shot, calculating and measuring to a target of 5-5.5 pH? Are you sure you want to dilute you beer with a liter of water, or are you going to reduce it to a cup or so during the boil?
I would try that, and then measure how much volume boiled water with extract you've got. Measure how much beer is left in your keg (ways to do this in beersmith I think using weight). Then pour a glass, and add the bitter extract in small measurable amounts, maybe 1 ml at a time. Stir and taste until the right number of drops have been added to taste. Then you could calculate how much of you concentrated boiled isomerized extract to add to your keg without going over your desired bitterness.
Let us know what happens. I've never tried this before.