The connection between Residual Neural Networks (ResNets) and continuous-time control systems (known as NeurODEs) has led to a mathematical analysis of neural networks, which has provided interesting results of both theoretical and practical significance. However, by construction, NeurODEs have been limited to describing constant-width layers, making them unsuitable for modelling deep learning architectures with layers of variable width. In this paper, we propose a continuous-time Autoencoder, which we call AutoencODE, based on a modification of the controlled field that drives the dynamics. This adaptation enables the extension of the mean-field control framework originally devised for conventional NeurODEs. In this setting, we tackle the case of low Tikhonov regularisation, resulting in potentially non-convex cost landscapes. While the global results obtained for high Tikhonov regularisation may not hold globally, we show that many of them can be recovered in regions where the loss function is locally convex. Inspired by our theoretical findings, we develop a training method tailored to this specific type of Autoencoders with residual connections, and we validate our approach through numerical experiments conducted on various examples.