Deep Learning (DL) has been utilized pervasively in the Internet of Things (IoT). One typical application of DL in IoT is device identification from wireless signals, namely Non-cryptographic Device Identification (NDI). However, learning components in NDI systems have to evolve to adapt to operational variations, such a paradigm is termed as Incremental Learning (IL). Various IL algorithms have been proposed and many of them require dedicated space to store the increasing amount of historical data, and therefore, they are not suitable for IoT or mobile applications. However, conventional IL schemes can not provide satisfying performance when historical data are not available. In this paper, we address the IL problem in NDI from a new perspective, firstly, we provide a new metric to measure the degree of topological maturity of DNN models from the degree of conflict of class-specific fingerprints. We discover that an important cause for performance degradation in IL enabled NDI is owing to the conflict of devices’ fingerprints. Second, we also show that the conventional IL schemes can lead to low topological maturity of DNN models in NDI systems. Thirdly, we propose a new Channel Separation Enabled Incremental Learning (CSIL) scheme without using historical data, in which our strategy can automatically separate devices’ fingerprints in different learning stages and avoid potential conflict. Finally, We evaluated the effectiveness of the proposed framework using real data from ADS-B (Automatic Dependent Surveillance-Broadcast), an application of IoT in aviation. The proposed framework has the potential to be applied to accurate identification of IoT devices in a variety of IoT applications and services. Data and code available at IEEE Dataport (DOI: 10.21227/1bxc-ke87) and \url{https://github.com/pcwhy/CSIL}}.