  In a $\beta$-Mn-type chiral magnet Co$_9$Zn$_9$Mn$_2$, we demonstrate that
the magnetic field-driven collapse of a room temperature metastable topological
skyrmion lattice passes through a regime described by a partial topological
charge inversion. Using Lorentz transmission electron microscopy, the
magnetization distribution was observed directly as the magnetic field was
swept antiparallel to the original skyrmion core magnetization, i.e. negative
magnetic fields. Due to the topological stability of skyrmions, a direct
transition of the metastable skyrmion lattice to the equilibrium helical state
is avoided for increasingly negative fields. Instead, the metastable skyrmion
lattice gradually transforms into giant magnetic bubbles separated by $2\pi$
domain walls. Eventually these large structures give way to form a
near-homogeneously magnetized medium that unexpectedly hosts a low density of
isolated skyrmions with inverted core magnetization, and thus a total
topological charge of reduced size and opposite sign compared with the initial
state. A similar phenomenon has been observed previously in systems hosting
ordered lattices of magnetic bubbles stabilized by the dipolar interaction and
called "topological melting". With support from numerical calculations, we
argue that the observed regime of partial topological charge inversion has its
origin in the topological protection of the starting metastable skyrmion state.
