The deep learning diagnosis of aircraft engine-bearing faults enables cost-effective predictive maintenance while playing an important role in increasing the safety, reliability, and efficiency of aircraft operations. Because of highly dynamic and harsh operating conditions of this system, such modeling is challenging due to data complexity and drift, making it difficult to reveal failure patterns. As a result, the objective of this study is dual. To begin, a highly structured data preprocessing strategy ranging from extraction, denoising, outlier removal, scaling, and balancing is provided to solve data complexity that resides specifically in outliers, noise, and data imbalance problems. Gap statistics under k-means clustering are used to evaluate preprocessing results, providing a quantitative estimate of the ideal number of clusters and thereby enhancing data representations. This is the first time, to the best of authors’ knowledge, that such a criterion has been employed for an important step in a preliminary ground truth validation in supervised learning. Furthermore, to tackle data drift issues, long-short term memory (LSTM) adaptive learning features are used and subjected to a learning parameter improvement method utilizing recursive weights initialization (RWI) across several rounds. The strength of such methodology can be seen by application to realistic, extremely new, complex, and dynamic data collected from a real test-bench. Cross validation of a single LSTM layer model with only 10 neurons shows its ability to enhance classification performance by 7.7508% over state-of-the-art results, obtaining a classification accuracy of 92.03 ± 0.0849%, which is an exceptional performance in such a benchmark.