Hydrothermal annealing can modify starch digestibility and techno-functional properties. This study evaluated annealing time (24–72 h; 67 °C, 70% moisture) in yellow sweet potato flour and starch subsequently recovered from the treated flours. In flour, rapidly digestible starch (RDS) decreased significantly (p < 0.05) from 41.5% in untreated flour to 37.5% after 72 h, with no significant differences among treated flours. Resistant starch (RS) increased significantly at each time, from 5.7% to 14.3% at 72 h. Total phenolic content and antioxidant activity decreased significantly after 24 h and partially recovered thereafter, remaining below untreated flour values. In recovered starch, RDS decreased significantly from 77.3% to 70.6%; the 48- and 72-h samples were significantly lower than the 24-h sample but did not differ from each other. RS increased from 17.3% to 25.5% and 25.8% at 48 and 72 h, respectively, without significant differences between these times. Descriptive analysis of single-run Rapid Visco Analyzer (RVA) profiles indicated less pronounced peaks during heating and greater viscosity development during cooling in both ingredients. Recovered-starch gel hardness decreased from 1.98 N to 0.83 N at 48 h. These findings characterize time-dependent changes in digestibility in both ingredients, gel texture in recovered starch, and phenolic content and antioxidant activity in flour, alongside observed changes in pasting behavior.