In complex transition metal oxides (TMO) an arrested electronic phase separation (PS) appears by tuning the system near a Lifshitz transition in multiband Hubbard models. The PS in La2CuO4+y near insulator to metal transition (IMT) is made of short range Charge Density Wave (CDW) order inhomogeneity coexisting with quenched lattice disorder. While at high doping y = 0.1 percolation gives a single superconducting phase, near the IMT at y = 0.06 two coexisting superconducting phases appear: the first one with a critical temperature Tc1 = 16 K and the second one with Tc2 = 29 K. It is known that the two superconducting phases are characterized by two different space geometry because of two different spatial distributions of both CDW order and dopants self-organization. Here we show that these two phases show different flux dynamic regimes using alternating current (AC) multi-harmonic susceptibility experiments. This is a unique technique capable to investigate multi-phase superconductors and characterize their transport properties in a percolative scenario. Results point out that the low critical temperature phase is well described by a bulk-like flux pinning with a 2D geometry while the phase with higher critical temperature shows a 'barrier pinning' mechanism providing direct evidence of two different superconducting vortex dynamics in different complex geometrical spaces.