It depends on which layer you are pointing within Blue Kenue. If you are talking about a layer called "BOTTOM" or "FOND" that is really the bathymetry (or topography) layer which will be described in Telemac by the variable ZF%R.
Furthermore, the only case where the bathymetry is changed during Telemac-2D simulation (No sisyphe coupled with it) is when the option "BOTTOM SMOOTHINGS" is activated (put not equal to zero). So, verify if this option is activated, and in that case, ZF will be changed compared to what was introduced in the geometry file.
With my best regards
Riadh ATA