Are you sure it is a Podocarpus and not a Ficus Alii? Hard to tell from the photos.
By definition, bonsai's are miniaturized plants that are designed to be kept very potbound and in the same small ceramic pot virtually forever. Sometimes, the roots need pruning as does the plant, but it should never be moved to a larger pot. If it is, it is no longer a bonsai.
The dry foliage is due to water stress. That can occur if the soil is allowed to get too dry between waterings. Ironically, it can also happen when the soil is not allowed to dry sufficiently and the roots rot. Rotted roots are dead roots that are no longer able to absorb water for the plant so the net effect is the same as if you had under-watered.
The foliage will not recover. My advice is to prune back all of the stems and move the plant back to a sunny windowsill and water when the top quarter of the soil is dry. If there are any healthy roots remaining, then you should see some healthy new growth emerge from the cut back stems.
