Unfortunately you can't get your track-point data back if you have already closed this workspace or project, although if you haven't you can undo the delete within the same project view. Tracks within a project view are linked to the tracks within the workspace - sometimes it is easier to edit points within a project view showing multiple tracks than it is to edit tracks individually. Unless you have a backup of your workspace database then I am afraid there isn't anything that can be done to restore this data.
As far as the palette is concerned, you are right in that it is not easy to specify specific colours to depths. If you are using AT5 colours, in particular, there is no interpolation between colours as the units can only use fixed colours. In this case, you could try setting up 12 colours (the number of colours in a palette) and then using a fixed depth range in the project of, say, 0-12m. This should (in conjunction with a 1m contour interval) give a distinct colour to every 1m interval between 0-12m, with everything over that being the same colour as the 12m band.