Manually replacing phoneme with another phoneme outside of the usual phoneset causes that phoneme to be skipped

My voicebanks use [ff] and [wr] instead of the usual [f] and [r] due to cross-language compatibility. Replacing the usual outputs (i.e. “run” being [r ah n]) to my own system’s phonemes (“run” being [wr ah n]) causes the audio output to entirely skip this phoneme during processing (“run” sounds identical to a note only containing [ah n]