I.e. on
https://petab.readthedocs.io/en/latest/documentation_data_format.html#condition-table
The NaN case is listed for speciesID but not for compartmentID and parameterID. It is unclear what happens here, but I assume the initial values of the model should be taken.
The sentence
the values will override any parameter values specified in the model.
reads for me, that you have to set the NaN.
See also discussion in AMICI-dev/AMICI#1796