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Here are the instructions for running the SW/FW co-simulation using Rogue + VCS:
https://github.com/slaclab/lcls2-pcie-apps/tree/lcls2-pgp-fw-lib-update/software/TimeTool#how-to-run-the-rogue-pyqt-gui-with-vcs-firmware-simulator 

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re-syncing

I would avoid the hardReset command. If you do a hardReset or lose link, I would do the following:
1) set EventBuilder.Blowoff to True
2) Turn off the fiber triggers (Hardware.Timing.Triggering.LocalTrig[0]EnableTrig = False)
3) Set EventBuilder.Blowoff to False
4) Turn back on the triggering (Hardware.Timing.Triggering.LocalTrig[0]EnableTrig = True)