OK, if the colour is the problem, ask Booxstor to do the colour user selectable (at least one global colour, not necesserily colour for each highlight..).
Or at least let the current default colour change to something else. (Should not be more than few minutes of work...)
It would solve your problem with new highlights. The old probably have the colour assigned and stored somewhere in sgl database. Someone might write the script to alter the colour data in database...