The task of blind source separation (BSS) involves separating sources from a mixture without prior knowledge of the sources or the mixing system. Single-channel mixtures and non-linear mixtures are a particularly challenging problem in BSS. In this paper, we propose a novel method for addressing BSS with single-channel non-linear mixtures by leveraging the natural feature subspace specialization ability of multi-encoder autoencoders. During the training phase, our method unmixes the input into the separate encoding spaces of the multi-encoder network and then remixes these representations within the decoder for a reconstruction of the input. Then to perform source inference, we introduce a novel encoding masking technique whereby masking out all but one of the encodings enables the decoder to estimate a source signal. To this end, we also introduce a sparse mixing loss that encourages sparse remixing of source encodings throughout the decoder and a so-called zero reconstruction loss on the decoder for coherent source estimations. To analyze and evaluate our method, we conduct experiments on a toy dataset, designed to demonstrate this property of feature subspace specialization, and with real-world biosignal recordings from a polysomnography sleep study for extracting respiration from electrocardiogram and photoplethysmography signals.