Hello Fabien,
INTENT IN only means that variables declared with such arguments can only be read, not changed in this subroutine.
Copy this FLUXPR_TELEMAC2D in your FORTRAN FILE and implement directly what you want inside this subroutine. If all needed variables are available in this subroutine, it is OK. Otherwise if they are variables known in declarations_telemac2d, you can add them on the line USE DECLARATIONS_TELEMAC2D, ONLY after NSE_FPR.
Otherwise, copy FLUXPR_TELEMAC2D in your FORTRAN FILE with a different name, e.g. FLUXPR_TELEMAC2D_2, call it in FLUSEC_TELEMAC2D with the new name FLUXPR_TELEMAC2D_2 and change the number of arguments to get new variables computed in FLUXPR_TELEMAC2D_2 you want (and delete the INTENT IN mentions). Then you can do and get whatever you want.
Hope this helps,
Chi-Tuan