It depends on exactly what you want to determinate and which accuracy you want to reach. Every system has its own time for reaching steady state when there is a heat flow variation, but also has its own fluctuations due to their construction and inevitable external factors.
You can estimate statistically fluctuations related to your system taking data without heat flux increment. So, when you begin to take data with heat flux increments, you can determinate the time when fluctuations reduce to those only due to your system construction and inevitable fluctuations. Hope this will help you