You need to add a few details, by your question I assume that your HDD has three partitions (c, d, and e), correct?
If so, you simply need to reformat the specific partition for reuse after you do a clean install of Windows with only the SSD attached, then reattach the HDD and delete its old C partition by any number of methods. One simple one is to use disk management and select the desired partition and format it or unpartition it and add its space to an adjacent partition.