This paper presents an area-driven Field-Programmable Gate Array (FPGA) scrubbing technique based on partial reconfiguration for Single Event Upset (SEU) mitigation. The proposed method is compared with existing techniques such as blind and on-demand scrubbing on a novel SEU mitigation framework implemented on the ZYNQ platform, supporting various SEU and scrubbing rates. A design space exploration on the availability versus data transfers from a Double Data Rate Type 3 (DDR3) memory, shows that our approach outperforms blind scrubbing for a range of availability values when a second order polynomial IP is targeted. A comparison to an existing on-demand scrubbing technique based on Dual Modular Redundancy (DMR) shows that our approach saves up to 46% area for the same case study.