A large-scale dataset is essential for training a well-generalized deep-learning model. Most such datasets are collected via scraping from various internet sources, inevitably introducing duplicated data. In the symbolic music domain, these duplicates often come from multiple user arrangements and metadata changes after simple editing. However, despite critical issues such as unreliable training evaluation from data leakage during random splitting, dataset duplication has not been extensively addressed in the MIR community. This study investigates the dataset duplication issues regarding Lakh MIDI Dataset (LMD), one of the largest publicly available sources in the symbolic music domain. To find and evaluate the best retrieval method for duplicated data, we employed the Clean MIDI subset of the LMD as a benchmark test set, in which different versions of the same songs are grouped together. We first evaluated rule-based approaches and previous symbolic music retrieval models for de-duplication and also investigated with a contrastive learning-based BERT model with various augmentations to find duplicate files. As a result, we propose three different versions of the filtered list of LMD, which filters out at least 38,134 samples in the most conservative settings among 178,561 files.