OK, I've found a rough way of doing it lol.
1. Select FPse
2. Select a game and wait for it to start
3. Press Menu and select eject
4. Press Back to remove game select menu
5. Press Menu again and select Quit, then restart
This should boot the PS as it would with no game inserted, I managed to copy and delete files like normal.
That method may have worked previously, but i dont't think it works with current version of FPSE - it doesn't work for me now with 11.29. When I eject, it wants to load a new iso, and if I don't choose anything and I then go to restart it asks me for an iso to load.
Yeah am wondering the same thing to, ive emailed the Dev and am waiting to hear back