There is an option for partial transfers in the TD Ameritrade transfer form. However, this is a manual process, via DocuSign. Jemstep Advisor Pro doesn't automatically support this functionality. Jemstep Advisor Pro only supports full transfers.
If an investor wants to execute a partial transfer, you would have to send the required partial transfer documentation to the investor manually, via DocuSign. Another option is to hold certain assets that the investor does not want to sell. When the investor completes the enrollment process, the assets will be in your care at TD Ameritrade. You (the advisor) have full control over the sell and buy trades. You may simply decide to hold certain assets that the investor does not want to sell.