Design note from Texas Instruments on technique in resetting and negative voltage generation from current transformers. Link here (PDF)
Transformers are used extensively for current sensing because they can monitor currents with very low power loss and they have wide bandwidth for good waveform fidelity. Current transformers perform well in applications with symmetrical AC currents such as push-pull or full bridge converter topologies. In single-ended applications, especially boost converters, problems can arise because of the need to accurately reproduce high duty factor, unipolar, waveforms. Unipolar pulses may saturate the current transformer and, if this happens, overcurrent protection will be lost and, for current mode control, regulation will be lost and an over voltage condition will result.