Build systems are fundamental to modern software development, but maintaining correct dependency specifications remains a significant challenge. Dependency-related errors, including missing and redundant dependencies, account for over 50% of build errors in large-scale software projects. Existing tools for detecting such errors suffer from two major limitations: high runtime overhead due to ptrace-based system call tracing, and the need to verify all edges in the build dependency graph. This paper presents mkcheck2, a novel approach that combines extended Berkeley Packet Filter (eBPF)-based system call tracing with incremental analysis to enable efficient dependency verification. Our evaluation on a diverse set of open-source projects demonstrates that mkcheck2 reduces the overhead of dependency error detection by up to 99.7% compared to existing ptrace-based approaches while maintaining detection accuracy. Across the entire 300-project Make corpus, the incremental analysis technique lowers the mean analysis time per commit from 1267.49 seconds to just 23.56 seconds, making continuous dependency verification practical in real-world development environments.