This only occurs when switching an import process from Primary Lookup ID to Alternate Lookup ID, and back again. To avoid this error, determine whether you are importing the Primary or Alternate lookup ID prior to beginning the import, and import it with the ID type that matches what exists in your file.
If you want to re-use an import process in the future, do not switch back and forth between different lookup ID types. Instead, create a distinct import processes specific for each ID type to be re-used. (i.e., create a re-usable "Lookup ID" process and a re-usable "Alternate Lookup ID" import process. do not create one process that switches back and forth)