You can set the internal samplerate of Stage Traxx in Settings > Playback Settings. If you import any tracks that don't match this setting, you will get the warning. If you ignore the warning you will most likely run into synchronization issues after some time. Maybe after 20 minutes, maybe after an hour or even later. But they will surely occur at some point.
Make sure all your songs have the same samplerate and set the internal samplerate of Stage Traxx to that.