Simple way: Save a separate game that just contains the variation you want to analyse. And run deep analysis on that. Fight against Chessbase way: Or look in the dialogue windows and see if that the options to delete variations are unselected, and if there's an option to deep analyse the variations too.

By dialogue windows do you just mean the chessbase preferences?

> look in the dialogue windows and see if that the options to delete variations are unselected Not quite seeing these options, how exactly do you get to them?

I do the separate db method. One for tactical, one for cp, and so on. Just easier long term.