If you edit the sequence in Premiere Pro while editing in Cutback, those changes will not be reflected in Cutback. Therefore, you’ll need to generate a new transcript based on the updated sequence.
To create a new transcript from the modified sequence, select [Transcribe] > [Transcribe again]. This will overwrite the existing Cutback project file, and it cannot be recovered. After generating the new transcription, you can re-edit it as needed and apply it to the sequence again.
If you resume editing in Cutback after modifying the sequence, it will no longer be synced with the previous transcript. You must generate a new transcript. If you want to preserve the previous work, save a copy of the original project before editing, or create a new sequence for the updated version.