Take notes on paper with fountain pen, take a picture, OCR it, shred the paper.
Otherwise there's literally nothing special about using a fountain pen for any task a pen can do (other than situations involving particular kinds of paper, like carbon paper or thin scratch pads).
If the convenience of doing notes digitally works better for you, then it is. You can still take out a fountain pen for a variety of other tasks (writing letters, calligraphy work for greeting cards), or recognize that for the time being there's little in your life that a fountain pen fills practically and just enjoy using one as a hobby