Hello Brad,
To answer your question, your channels, tasks, and scales should not disappear from MAX when you perform an export. However, the export option in MAX only applies to DAQmx configurations, tasks, scales, and global channels. To save your Traditional NI-DAQ configurations, navigate to Tools >> Traditional NI-DAQ Configuration.
As far as the missing channels are concerned, perhaps someone imported a blank configuration file. Regardless, the channels should not have disappeared from performing an export.
I hope this helps!
Matthew C
Applications Engineer
National Instruments