A new iterative algorithm for solving initial data inverse problems from partial observations has been recently proposed in Ramdani et al. (Automatica 46(10), 1616-1625, 2010). Based on the concept of observers (also called Luenberger observers), this algorithm covers a large class of abstract evolution PDE's. In this paper, we are concerned with the convergence analysis of this algorithm. More precisely, we provide a complete numerical analysis for semi-discrete (in space) and fully discrete approximations derived using finite elements in space and an implicit Euler method in time. The analysis is carried out for abstract Schrödinger and wave conservative systems with bounded observation (locally distributed).