In this study, we aim to offer linguistically motivated solutions to resolve the issues of the lack of representation of null morphemes, highly productive derivational processes, and syncretic morphemes of Turkish in the BOUN Treebank without diverging from the Universal Dependencies framework. In order to tackle these issues, new annotation conventions were introduced by splitting certain lemmas and employing the MISC (miscellaneous) tab in the UD framework to denote derivation. Representational capabilities of the re-annotated treebank were tested on a LSTM-based dependency parser and an updated version of the BoAT Tool is introduced.