Hi,
There shouldn't be any negative water surface change while doing floodplain encroachment. The negative change in water surface means that you squeeze too much on the water. The velocity of water will increase and water surface will drop and will be going towards supercritical flow.
You have to encroach the water by lesser amount as you did in your current project. If you encroach by lesser amount the problem you faced will be solved.
Thanks,
Debajit Basu Ray
debajit@bossintl.com