The prototypical system for understanding doping in solution-processed organic electronics has been poly(3-hexylthiophene) (P3HT) p-doped with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ). Multiple charge-transfer states, defined by the fraction of electron transfer to F4TCNQ, are known to coexist and are dependent on polymer molecular weight, crystallinity, and processing. Less well-understood is the loss of conductivity after thermal annealing of these materials. Specifically, in thermoelectrics, F4TCNQ-doped regioregular (rr) P3HT exhibits significant conductivity losses at temperatures lower than other thiophene-based polymers. Through detailed spectroscopic investigation of progressively heated P3HT films coprocessed with F4TCNQ, we demonstrate that this diminished conductivity is due to formation of the nonchromophoric, weak dopant HF4TCNQ-. This species is likely formed through hydrogen abstraction from the α aliphatic carbon of the hexyl chain at the 3-position of thiophene rings of rr-P3HT. This reaction is eliminated for polymers with ethylene glycol-containing side chains, which retain conductivity at higher operating temperatures. In total, these results provide a critical materials design guideline for organic electronics.