The answer relay in the way chessbase has build the three.
The old obk three was build like this:
and so on like a spreadsheet. Now if visually it may seem similar to ctg the threes where independent from each other, meaning that I could change the value of a move without effecting any other part of the three.
In ctg the threes are build more like a series of arrays.
So we have the board (a1 to h8), the pieces (p to K), the move number (0, 1, 2 etc), the symbols (!, ? etc) and the colour (red, green).
In my experience the array as been arranged without thinking of the independence of the three lines.
The emphasis has been given on the actual move (say Na3), and the colour, while the move number seems not to have any weight. What this mean? It means that if I change the colour of the move in a particular three (or more than in one three) all threes with that move will finish to have the same colour. This is valid also if you delete a move from some threes, it will disappear from all.
The conclusion is that the more you tweak a book the possibility to get into wrong lines without releasing why. The solution is in a better 'screening' of the games you import to make the book and to tweak it 'wisely'...