If you miss the timing it is not Agnihotra and you will not get the healing effect on the atmosphere or in the ash.
After each Agnihotra try to spare as many minutes as you can for meditation. You can sit at least till the fire extinguishes itself. Agnihotra creates a medicinal and healing atmosphere.
Just before the next Agnihotra collect the ash and keep it in a glass or earthen container. It can be used for plants or making folk medicines