I don't think any Ayurvedic or any other medicine system will take care of your lipoma
swelling. I have seen people who live with them.
The only treatment as you know is excision only which can be done if it bothers you cosmetically or it becomes painful or restricts movements.And and far as I know, there is no relation between weak digestion and lipoma.
hope my info helped you
Dr Hari Om Chandrakar