Large scale inference models are widely used in neuroscience to extract latent representations from high-dimensional neural recordings. Due to the statistical heterogeneities between sessions and animals, a new model is trained from scratch to infer the underlying dynamics for each new dataset. This is computationally expensive and does not fully leverage all the available data. Moreover, as these models get more complex, they can be challenging to train. In parallel, it is becoming common to use pre-trained models in the machine learning community for few shot and transfer learning. One major hurdle that prevents the re-use of generative models in neuroscience is the complex spatio-temporal structure of neural dynamics within and across animals. Interestingly, the underlying dynamics identified from different datasets on the same task are qualitatively similar. In this work, we exploit this observation and propose a source-free and unsupervised alignment approach that utilizes the learnt dynamics and enables the re-use of trained generative models. We validate our approach on simulations and show the efficacy of the alignment on neural recordings from the motor cortex obtained during a reaching task.