Magnetic skyrmions are key candidates for applications in memory, logic and neuromorphic computing. An essential property is their topological protection that is caused by the swirling spin texture and described by a robust integer winding number. However, this protection is strictly enforced only in the continuum, and so the atomic lattice present in all real materials leaves a loophole for switching the winding number. Hence, understanding the microscopic mechanism of this unwinding is crucial for enhancing the stability of skyrmions. Here we use spin-polarized scanning tunnelling microscopy to locally probe skyrmion annihilation by individual hot electrons. We tune the collapse rate by up to four orders of magnitude by using an in-plane magnetic field, and observe distinct transition rate maps that either are radial symmetric or exhibit an excentric hotspot. We compare these maps to atomistic spin simulations based on parameters obtained from first-principles calculations and find that the maps are explained by a radial symmetric collapse at zero in-plane magnetic field and a transition to the recently predicted chimera collapse at finite in-plane magnetic fields. These insights into the transient state of the skyrmion collapse will enable future enhancement of skyrmion stability and designs for intentional skyrmion switches.