Stability analysis is needed to maximize milling performance while avoiding chatter. However, such an analysis is time-consuming, requiring the use of sophisticated instrumentation, and has significant level of uncertainty, which impedes the widespread use by industry. A main source of uncertainty is believed to be the changes in dynamics of the tool-holder-spindle system during the milling operation. This study investigates the variation in the tool point dynamics reflecting the dynamics of the tool-holder-spindle system and associated machining stability. The investigation focuses on the effects of the conditions generated by typical milling operations, such as tool changes and spindle warm up. The results of analyses demonstrate the necessity of continuous updates of the tool point dynamics during milling process by in-situ measurements to minimize uncertainty in evaluation of machining stability.