Ferroelectric field-effect transistor (FeFET)-based compute-in-memory (CIM) promises energy-efficient deep neural network (DNN) inference, but device variation can severely degrade bit-sliced CIM accuracy. Prior works either rely on hardware modifications or treat such variation as generic noise, overlooking a key FeFET asymmetry: negligible off-state leakage makes errors dominated by conducting on-state cells. This asymmetry is amplified by two's-complement sign extension, which maps small negative values to high-significance bit slices and magnifies their errors during shift-and-add reconstruction. In this paper, we propose CAFE, a conducting-cell-aware adaptive differential encoding framework built upon this FeFET-specific asymmetry. CAFE introduces C$^2$AM, a bit-significance-weighted conducting-cell activity metric that predicts output deviation and inference accuracy degradation under FeFET device variation. Guided by C$^2$AM, CAFE applies differential weight and activation encoding to eliminate sign-extension-induced conducting-cell amplification. To balance robustness and cost, CAFE performs type-wise encoding enumeration, layer-wise NSGA-II search, and post-GA pruning to allocate robust encodings where the robustness-cost trade-off is favorable. Across representative vision and language workloads, CAFE reduces C$^2$AM by up to $28.6\times$; in the main deployment study, it improves accuracy over two's-complement CIM by more than 87 percentage points and approaches full-differential robustness at $1.86$-$2.78\times$ normalized cost, compared with $3.06\times$ for uniform full-differential encoding.

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