Skyrmion crystals are regular arrangements of magnetic whirls that exist in a wide range of chiral magnets. Because of their topology, they cannot be created or destroyed by smooth rearrangements of the direction of the local magnetization. Using magnetic force microscopy, we tracked the destruction of the skyrmion lattice on the surface of a bulk crystal of Fe1-xCoxSi (x = 0.5). Our study revealed that skyrmions vanish by a coalescence, forming elongated structures. Numerical simulations showed that changes of topology are controlled by singular magnetic point defects. They can be viewed as quantized magnetic monopoles and antimonopoles, which provide sources and sinks of one flux quantum of emergent magnetic flux, respectively.