Hi stingrayRF,
Unfortunately, the NI 5112 will not allow you to abort an acquisition in progress without resetting the absolute reference timer.
In the future, you may want to consider the NI 5122/5124/5922 SMC based products, as they will allow you to abort an acquisition without resetting the absolute reference timer. These new products also support many advanced options that the 5112 does not, such as the ability to synchronize and trigger independently without the use of an external device to calibrate the absolute timestamp counters.
Sorry for the bad news. Best regards,
Chad AE
Applications Engineer