The only source of non-volatile memory on the FPGA is the flash. The document linked below discusses how to Erase the FPGA flash memory:
Erasing FPGA Flash Memory
Any other type of memory should be cleared by simply cycling power to the card. If you want to verify that the bitfile has been cleared, you can follow these steps:
1) Deploy a "blank" bitfile to the fpga with the bitfile set to run when downloaded
By "blank" I mean a bitfile that has just 1 front panel indicator on it so you can check that the bitfile is deployed.
2) Have the host open reference, but do not "run"
3) Check the front panel read/write indicator.
4) If it reads successfully, then you know that your FPGA has the "blank" vi on it (i.e. it has been cleared of all other information except this "blank" VI).
Hope that helps!
Regards,
Ryan K.
Product Manager, ATCA and BEEcube
National Instruments