That actually a popup prompt fired up when you click Generate Skeleton in Accurig.
However, if you import FBX without mapping bones in Characterization, you are going to have a "raw" (non-functional) rig without face bones ID.
Running Accurig at this point would create a fresh rig and not ask to preserve a face rig, because there would be none.
Importing blend-shapes at this point would be hard to impossible.
So my advise is to map bones on import in Characterization and Activate it (even if you are not going to use it).
Face rig would automatically be identified (even if it is as simple as a single head bone).
Then import blend-shapes through Expression Editor from the same FBX.
Finally run Accurig and select to keep existing face set.