I apologize for the trouble you're having with this model. In all honesty, we did not consider the situation you're trying to model.

You are correct in assuming that since WAVx is specified in the load cases, buoyancy is being considered throughout.

Switching wave off for a section of the pipe will eliminate the wave loads, but if the pipe is really submerged buoyancy should still be considered. Perhaps a better way to get close to where you want to be would be to adjust the hydrodynamic parameters (which we usually advise to leave blank). Here is a suggestion:

1) Within the Load Case Editor, go to the particular wave dialog you're interested in and view the wave table. For your pipe(s), note the particle velocities.
2) Manually determine (from charts) the values of Cd, Cm, and Cl.
3) On the first element subjected to wave loading, specify Cd, Cm, and Cl. On the first element NOT subjected to wave loading reset these coefficients to a small value - something like 0.02. Later in the model when the piping is subjected to wave loading, reset the coefficients to the values from the charts.

Cautions
1) Do not set the coefficients to zero, that is the same as leaving them blank. CAESAR II would then determine their values as usual which is not what you want on the sections that don't see the wave loading.
2) I do not remember the "small value cut-off", below which CAESAR II will assume no entry and determine the coefficients. Build a 1 or 2 element model and play with the coefficients to determine this.
3) Remember that wind/wave loading is duplicated forward, just like allowable stresses and uniform loads. You do not have to specify this data on every element - only where it changes.