I am trying to estimate multiple propagation parameters along with orbital parameters using EKF(eg. SRP-reflection coefficient and Drag CD). I would like to know how Orekit sets the sequence of the parameters in the state vector within its code. For example when specifying the covariance matrix values and initial state for the propagation parameters which parameter comes first?
( I could not find documentation regarding this). It seems the order is not related to the force models that are added to the propagator.

I think you can get them from getPropagationParametersDrivers in KalmanEstimator. There are also methods getOrbitalParametersDrivers and getEstimatedMeasurementsParameters. If I remember correctly, we put first all orbital parameters, then all force parameters, then all measurements parameters. Inside the propagation and measurements parameters, I think we order them lexicographically (within each list, but the two lists are one after the other), for the sake of reproducibility. For orbital parameters, we use a fixed ordering that should correspond to the order of parameters in the orbit constructors.