@Diarmuid Collins The "digital" mode is not a digital plot, signals are displayed as analog waveforms, it only means signals are displayed in stacked order instead of overlapped. However as you might notice the Y resolution of each signal is reduced.
If you place the mouse pointer to the left, close to the Y axis and use the mouse wheel with Shift pressed you can increase/decrease the height of the signals (it's like a vertical zoom).
If you increase too much the signal name does probably get truncated as it is scaled too.(see image).
The Ymin - Ymax should always be set to the min-max voltage level of the signals in the graph. If you set a lower value xschem allocates space for that voltage range, if signals go beyond that you see vertical overlaps.
You never lose signals, they might not fit into the graph area. Placing the mouse to the left of the y axis, pressing left button and moving the mouse vertically you drag the signals up and down, so you can bring out of view signals back in.
To see all signals either zoom vertical (as explained above) to make signals smaller in Y direction or increase the graph size.