Pcsx2 Save Game Location ((new)) -

C:\Users\YourUsername\AppData\Roaming\PCSX2

Recent versions of PCSX2 (1.7+ / Qt interface) may also use: C:\Users\[YourUsername]\AppData\Roaming\PCSX2\memcards\ (Windows) Check both if your saves seem missing. pcsx2 save game location

Keep in mind that you can change the save game location by modifying the PCSX2 settings. To do this: pcsx2 save game location