Abstract: This paper considers reliable in-sequence molecular communication, where bio-nanomachines exchange molecule-encoded information in a specified order, and investigates a new simulation-based method to incrementally evaluate communication protocols by gradually increasing the complexity of experimental settings. The proposed method, called Affine Memory Replay (AMR), builds a continual learning (CL) model to estimate communication performance between bio-nanomachines. AMR stores past simulation samples and synthesizes additional replay samples through interpolation and extrapolation between past samples. Through incremental performance estimation tasks, it replays both past and synthetic samples to regularize model updates, helping the model adapt to new experimental settings while retaining knowledge from earlier ones. Experimental results show that AMR significantly outperforms existing CL methods in maintaining overall estimation accuracy across sequentially learned estimation tasks. It effectively balances memory stability and learning plasticity under moderate training cost.