In many retrieval systems the original high dimensional data (e.g., images) is mapped to a lower dimensional feature through a learned embedding model. The task of retrieving the most similar data from a gallery set to a given query data is performed through similarity comparison on features. When the embedding model is updated, it might produce features that are not comparable/compatible with features already in the gallery computed with the old model. Subsequently, all features in the gallery need to be re-computed using the new embedding model -- a computationally expensive process called backfilling. Recently, compatible representation learning methods have been proposed to avoid back-filling. Despite their relative success, there is an inherent trade-off between new model performance and its compatibility with the old model. In this work, we introduce FastFill: a compatible model update process using feature alignment and policy based partial backfilling to promptly elevate retrieval performance. We show that previous backfilling strategies suffer from decreased performance and demonstrate the importance of both the training objective and the ordering in online partial backfilling. We propose a new training method for feature alignment between old and new embedding models using uncertainty estimation. Compared to previous works, we obtain significantly improved backfilling results on a variety of datasets: mAP on ImageNet (+4.4%), Places-365 (+2.7%), and VGG-Face2 (+1.3%). Further, we demonstrate that when updating a biased model with FastFill, the minority subgroup accuracy gap promptly vanishes with a small fraction of partial backfilling.