The problem of repairing inconsistent knowledge bases has a long history within the communities of database theory and knowledge representation and reasoning, especially from the perspective of structured data. However, as the data available in real-world domains becomes more complex and interconnected, the need naturally arises for developing new types of repositories, representation languages, and semantics, to allow for more suitable ways to query and reason about it. Graph databases provide an effective way to represent relationships among semi-structured data, and allow processing and querying these connections efficiently. In this work, we focus on the problem of computing prioritized repairs over graph databases with data values, using a notion of consistency based on Reg-GXPath expressions as integrity constraints. We present several preference criteria based on the standard subset repair semantics, incorporating weights, multisets, and set-based priority levels. We study the most common repairing tasks, showing that it is possible to maintain the same computational complexity as in the case where no preference criterion is available for exploitation. To complete the picture, we explore the complexity of consistent query answering in this setting and obtain tight lower and upper bounds for all the preference criteria introduced.