The low-temperature charge-density-wave (CDW) state in the layered organic metals $alpha $-(BEDT-TTF)$_2$MHg(SCN)$_4$ has been studied by means of the Shubnikov -- de Haas and de Haas -- van Alphen effects. In addition to the dominant alpha-frequency, which is also observed in the normal state, both the magnetoresistance and magnetic torque possess a slowly oscillating component. These slow oscillations provide a firm evidence for the CDW-induced reconstruction of the original cylindrical Fermi surface. The alpha-oscillations of the interlayer magnetoresistance exhibit an anomalous phase inversion in the CDW state, whereas the de Haas -- van Alphen signal maintains the normal phase. We argue that the anomaly may be attributed to the magnetic-breakdown origin of the alpha-oscillations in the CDW state. A theoretical model illustrating the possibility of a phase inversion in the oscillating interlayer conductivity in the presence of a spatially fluctuating magnetic breakdown gap is proposed.