I don't think so. I think the Import XLS simply does an append to the current data set. I've always deleted all the records from the relevant tables using a DML ststement kicked off from a web script in the FDM Taskflow and then loaded a complete dataset from the template with whatever changes are necessary, additional records, updates deletes etc. It's clean and works.
If you have created the custom table in the FDM database/schema then yes. Just for information its best to open a new thread for your question rather than post on an already closed/answered thread as you will get a better response.