This study analyzes the longitudinal disparity Δt between Basic Literacy Rate (BLR) and Functional Literacy Rate (FLR) in the Philippines from 1989 to 2024, focusing on the impact of the 2024 methodological revision of the Functional Literacy, Education and Mass Media Survey (FLEMMS) by the Philippine Statistics Authority (PSA). A piecewise time-series approach was employed. The Old Regime (1989–2019) disparity was modeled using a linear trend analysis to determine the historical drift. The discontinuity introduced by the 2024 definition change was quantified as a structural break. The New Regime (2024 onwards) was analyzed and forecasted using a scenario-based Random Walk with Drift (ARIMA(0, 1, 0)) model. The Old Regime analysis showed that the disparity consistently closed at a statistically significant rate of 0.647 percentage points (pp) annually (R2 = 0.999). However, the 2024 FLEMMS, which required direct comprehension testing, established a new disparity of 22.3 pp, quantifying a 20.8 pp structural break in the series. This shift reveals a widespread national comprehension crisis that has been masked by less rigorous definitions. Forecasting under the "Optimistic" scenario (assuming the historical closure rate is maintained) projects that the disparity will remain high at 19.1 pp by 2029. The results necessitate a complete pivot in national education policy from ensuring basic literacy to addressing the vast comprehension gap. The study recommends accelerated, targeted interventions and a mandate for high-frequency (annual) FLEMMS data collection to enable statistically robust monitoring and effective policy response.