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To control the playback, use the VBS3 AAR time line and control.  You will see that VBS3Strike provides a timer dialog which shows the synchronization of VBS3Strike to VBS3.

Additionally, VBS3Strike injects the explosion effects into the VBS3 AAR at the correct time and place during AAR playback.  Due to the way the VBS3 engine operates in AAR mode, pausing the VBS3 AAR will not pause the injected particle effects.  Similarly rewinding will not remove any effects currently in progress.  Having said that, rewinding and playing back effects is possible, just ensure that enough time has passed to let the earlier generated effects dissipate.