Hello,
I had a look at both cases and what I see is not what you say in your post, please be more specific. In the "old" case I see a constant Chézy coefficient equal to 35., in the case "new" I see 6 zones of Chézy friction with coefficients ranging from 70. to 200., so this is less friction and you have accordingly larger velocities, that's all I can say. It is a case of a tide in a bay with very shallow flows in the upper part of the mesh, so probably high velocities when the tide comes in and high influence of friction.
The accuracy you ask for is also probably too rough, try 1.E-6 instead of 1.E-3.
With best regards,
Jean-Michel Hervouet