On Sept 21st 2020 there will be full overlap between Thanos data and Prometheus data. After that we should progressively reduce Prometheus' retention and increase Thanos coverage (i.e. the time span of queries that are served by Thanos)
Also note that ATM Prometheus compactions are disabled to be able to upload data to Thanos, meaning that queries to Prometheus that contain both a lot of metrics and long time ranges will be slower than usual.