Manually edit each line object
The easiest method would be to open the fig file, use the pointer to select the line you'd like to edit so that it is the current object, and then execute this line of code in the command window. 0.5 is the transparency level between 0 (invisible) and 1 (opaque).
set(gco, 'Color', [get(gco,'Color'), 0.5])
Programmatically edit all line objects on the axes
Another method is to get the handle from the axes programmatically but then you have to add additional steps to isolate the handle you'd like to change. If you'd like to set the transparency of all objects on the axes, select the axes so it's the current axis and then run this line from the command window. Again, 0.5 is the transparency level.
set(get(gca,'Children'),{'color'},cellfun(@(x)[x,0.5],get(get(gca, 'Children'),'color'),'UniformOutput',false))
The reason why the transparency levels aren't saved in the figure
The reason the transparency level doesn't appear when opening the figure is because this 4th element of the color vector is undocumented and isn't saved when saving the figure.
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