I hope you're doing well. Typically, if you want to set a new value to certain properties during run-time, you may be able to do so with DAQmx properties. You can get a list of what properties you can set by opening the NI-DAQmx C Reference Help in Windows by going to Start»Programs»National Instruments»NI-DAQ. Once you have the Help file open, expand the NI-DAQmx C Properties tree. The specific property you need to change your counter output frequency is "DAQmxSetCOFreq" which you can find under the List of Channel Properties and scrolling down to Counter Output. Every time you call this function, it will set your counter output frequency accordingly. Keep in mind that not all properties can be modified at run-time. Let us know if you have any additional questions!
Thaison V Applications Engineer National Instruments