Context. Stellar flybys in star clusters are suspected of affecting the orbital architecture of planetary systems causing eccentricity excitation and orbital misalignment between the planet orbit and the equatorial plane of the star. Aims. We explore whether the impulsive changes in the orbital elements of planets, caused by a hyperbolic stellar flyby, can be fully damped by the circumstellar disk surrounding the star. The time required to disperse stellar clusters is comparable to the circumstellar disk's lifetime. Since we perform 3D simulations, we can also test the inclination, excitation, and damping. Methods. We have modeled in 3D with the SPH code VINE, a system made of a solar-type star surrounded by a low density disk with a giant planet embedded in it approached on a hyperbolic encounter trajectory by a second star of similar mass and with its own disk. Different inclinations between the disks, planet orbit, and star trajectory have been considered to explore various encounter geometries. We focus on an extreme configuration where a very deep stellar flyby perturbs a Jovian planet on an external orbit. This allows us to test in full the ability of the disk to erase the effects of the stellar encounter. Results. We find that the amount of mass lost by the disk during the stellar flyby is less than in 2D models where a single disk was considered. This is mostly related to the mass exchange between the two disks at the encounter. The damping in eccentricity is slightly faster than in 2D models and it occurs on timescales on the order of a few kyr. During the flyby both the disks are warped owing to the mutual interaction and to the stellar gravitational perturbations, but they quickly relax to a new orbital plane. The planet is quickly dragged back within the disk by the tidal interaction with the gas. The only trace of the flyby left in the planet system, after about 10 4 yr, is a small misalignment, lower than 9 • , between the star equatorial plane and the planet orbit. Conclusions. In a realistic model based on 3D simulations of star-planet-disk interactions, we find that stellar flybys cannot excite significant eccentricities and inclinations of planets in stellar clusters. The circumstellar disks hosting the planets damp on a short timescale all the step changes in the two orbital parameters produced during any stellar encounter. All records of past encounters are erased.