It's a fairly straightforward issue, and there is a workaround, but this is still a bug that should be fixed.
If a clip is transcribed, but then replaced with a new file using 'replace footage', the source footage is updated, but the transcription and its timings remain from the original file. There's no way I can see to force Premiere to recognise that the original audio has changed - meaning the transcription should be updated - and there's no button to retranscribe a dynamic transcription after using 'replace footage'.
The workaround is simply to delete the audio track, import the new file's audio, and transcribe that. But this shouldn't be necessary. If a file's replaced and the audio has changed, then there should be the opportunity for the transcription feature to recognise that.