The recovery effect of isochronal thermal annealing and inelastic energy deposited during 100 MeV Ag swift heavy ion (SHI) irradiation is demonstrated in the case of 4H-SiC pre-damaged by elastic energy deposition of 300 keV Ar ion. The Ar-induced fractional disorder follows a nonlinear two-step damage build-up. The fractional disorder level of 0.3 displacements per atom (dpa) is established as the threshold above which the lattice rapidly enters the amorphous phase, characterized by the presence of highly photo-absorbing defects. The SHI-induced recovery suggests that the damage annealing, in the pre-damaged region (∼350 nm) where the Se for 100 MeV Ag is almost constant (∼16.21 keV/nm), is more pronounced than the damage creation by SHI. This allows the disorder values to saturate at a lower value than the present initial disorder. Furthermore, the thermal effect due to SHI irradiation of an amorphous nano-zone embedded in a crystalline host matrix has been evaluated using the 3D implementation of the thermal spike. The recovery process by SHI is ascribed to the thermal spike-induced atomic movements resulting from the melting and the resolidification of the crystalline–amorphous interface.