After you make your own timeline for YouTube video, you can use this to separate YouTube Auto VTT subtitle to ASS subtitle.
.Net 4.5 required
The judgement of whether the word time is between your timeline is base on word_time > your_timeline_start && word_time < your_timeline_end,
but it should be using Math.Abs(word_time - your_timeline_start) > a_ms_time_like_300ms, for as the youtube timeline could be a bit head of your own timeline.
To prevent from this happening of losing words, you can make your timeline a bit wider, which means the it starts a bit earlier, and ends a bit later.