I much prefer just keeping everything on the MiSTer SD card, and syncing it to a backup on my PC hard drive via the network. Any issues with the SD card, I can just recopy the data from the backup (or worst case, copy to a new card).
Haven't experienced any SD related issues in five years of MiSTer usage though. Did upgrade from 256GB to 512GB once; copying the data from backup to new card worked perfectly.