To remove an unwanted, duplicate, old, or unused data set, then the simplest way to accomplish this is to open the data set that you don't want anymore by going to File -> Open, to open it in Moneydance and verify that it is, indeed, the data set that you want to remove.
After opening it, if you're using a Mac, right click (or Ctrl + click) the Moneydance title bar, then select the folder directly below your data set to open the folder that contains your data set in Finder.
After doing that, Finder will open and the data set to be removed will be selected (note: in some instances, the data set will have a folder icon instead of the Moneydance icon).
Switch back to the Moneydance window and close Moneydance, then drag and drop the unwanted data set in the Finder window to your Trash folder (but don't empty it yet!).
After that, open Moneydance and you'll be brought to the Welcome screen, which will allow you to open your other data set(s). Select your current data set and open it in Moneydance and make sure that your data is correct (to ensure that you removed the correct data set). Once you've done that, you can safely empty your Trash folder! Repeat this process for any additional unwanted data sets.
If you're using Windows or Linux, the location of the data set will be in the Moneydance title bar, so you can use Windows Explorer (or your preferred Linux file manager) to browse to the location of your data set and find the yourfilename.moneydance data set, then close Moneydance and move it to your Trash folder and follow the instructions above after the Moneydance Welcome screen, to verify that you've removed the correct data set.