Period skipping will not cause the inductor to saturate. The basic idea is that in a power supply that never period skips, the pulses become narrower with decreasing load. At some point, the pulse has to be so narrow that a very significant amount of it is turning on and off the transistors. Efficiency drops as a result.
Now imagine if every other period is skipped, meaning that the output pulse is suppressed. Now the pulses are twice as large as before and the effective operating frequency halved, reducing losses. The pulses are still narrower than when the power supply is operating at full load, so inductor saturation does not occur. The low output current also means that the filter capacitors will be able to cope with the low frequency.
In reality, a 1:2 skip ratio is very low. My discrete design (2 transistors, but I forgot the details) had a skip ratio on the order of 1:1000, since it operates at about 25kHz and slows down to a pulse a few times a second at no load (only the load of the voltage sense circuit). It only pulls a few mW from the rectified AC line in that condition, not bad for a simple circuit! (If designs like that were used in the standby circuit of modern electronics, standby loss would be a lot less significant!)