Is there a way to split the embedded data in survey flow and store the split value as a separate embedded data?

Not in the survey flow but we can create a workflow for it which should be triggered on new response record. Under this workflow we will add a code task to get the required value from embedded data and then use webservice task to run the update response API to update the resulted value in the required embedded date. 

Using custom javascript in your first question, you can retrieve and parse the ED you want to split and store the values in new ED fields.

See https://api.qualtrics.com/82bd4d5c331f1-qualtrics-java-script-question-api-class for the question API.