Yes. You can try using the CRC function. It will calculate the CRC value of the data it was configured with and compare it to the CRC value generated by Quartus II during compilation. See AN 357 for more information on this feature.
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For Stratix, Stratix GX, Cyclone II, and Cyclone devices, the CRC is
computed by the Quartus II software and downloaded into the device as
part of the configuration bit stream. These devices store the CRC in the 32-
bit storage register at the end of the configuration mode.
When the error detection CRC feature is enabled in user mode, these
devices recalculate the CRC based on the contents of the device and
compare it against the 32-bit storage register.
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http://www.altera.com/literature/an/an357.pdf (
http://www.altera.com/literature/an/an357.pdf)