Once started recording, the machine will continue to record until the memory card is full. If recording at 24/96 it will start new files approximatley every hour or every two hours depending on how it is set. Starting new files more frequently is one hedge against file loss in the case power is lost or some other problem occurs. In that situation only the current file(s) being writen would be likely to have problems.
How long the machine will record to a file before starting a new one is determined by three factors: the bit-depth/sample-rate at which you are recording, how many channels are encoded in the file, and the file size limitation.
Here's each of those factors-
1) Recording at 24bit/96Khz produces 16.5 MB/min per channel. That's just under 1GB of data per hour.
2) The DR-680 can be set to write either single channel mono files (1 channel per file) or 2-channel interleaved-stereo files (2 channels per file) for the six analog input channels. 2-channel stereo interleaved files contain twice as much data as single channel mono files. (Note that the 'extra' digital-input or monitor-mix stereo channel is always a 2-channel stereo-interleaved file)
3) The file size limitation is 2GB. Once a file reaches this size, a new one is started by the recorder. This happens "seamlessly" meaning that there is no gap in recording, or in playback once the files are rejoined or played sequentially.
So if you are recording at 24bit/96Khz, and have the machine set to record single channel mono files, the machine will start a new file for each channel approximately every two hours.
If you set the machine to record 2-channel stereo files (which are always channel pairs- ch1&2, ch3&4, ch5&6), the machine will start new files for each channel pair approximately every hour
Either way, the stereo digital-input / monitor-mix file will always be a 2-channel stereo file and will start a new file approximately every hour.
If recording at 24/48 the data rate is half that of 24/96, so the file slits happen at just over 2 or 4 hour intervals instead of 1 or 2 hour intervals.
[edited to correct the data rates]