Convolutional neural networks (CNNs) are widely adopted in safety-critical systems, including space applications and autonomous vehicles. Field-programmable gate arrays (FPGAs) based on SRAM are preferred for accelerating CNN computations due to their unique characteristics. However, the configuration memory of FPGAs is susceptible to single event effects (SEEs), which can corrupt computations and lead to misclassification of CNN outputs. In this study, we investigated the impact of SEEs on SRAM-based FPGAs with Two-Photon Absorption (TPA) laser fault injections through a comparative analysis of two popular CNN acceleration architectures: streaming architecture (SA) and single compute engine (SCE). Experimental results show that SA-based CNNs require more hardware resources but exhibit superior resilience against single event upsets (SEUs). Without any Radiation Hardened by Design (RHBD) protection, SCE has an error rate approximately twice as high as SA. To mitigate errors, the Xilinx IP core - Soft Error Mitigation (SEM) is used for error detection and correction, leading to error rate reductions of up to 50 % in both architectures. Importantly, we propose the AutoDPR-SEM (Autonomous Dynamic Partial Reconfiguration for Soft Error Mitigation) approach, which automatically reconfigures the SEM IP core when it remains idle due to uncorrectable errors. AutoDPR-SEM significantly improves CNN error rates, reducing errors by approximately 17.8 times in SCE and 14.8 times in SA. We also applied software level simulation to validate the TPA experiment, showing similar trends of the testing results across all models. In conclusion, the study confirms the feasibility of AutoDPR-SEM in both architectures, showcasing its potential to improve CNN error rates in safety-critical systems.