Altera preferred to omit the clearer description in previous device handbook versions.
Now the information is hidden in Note (1) to table 12-3:
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Bus hold and weak pull-up resistor features override the high-impedance state of HIGHZ, CLAMP, and EXTEST.
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In previous versions, there was an explicite explanation of individual BST instructions affecting the IO states, e.g. for CLAMP:
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If you are testing after configuring the device, the programmable weak pull-up resistor or the bus hold feature overrides the CLAMP value (the value stored in the update register of the boundary-scan cell) at the pin.
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In any case, if you are in doubt about the real device behaviour, why don't you simply try it?