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 co-processed with F4TCNQ, we demonstrate that this diminished conductivity is due to formation of the non-chromophoric, weak dopant HF4TCNQ-. This species is likely formed through hydrogen abstraction from the alpha 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.