If you have deleted all your locations and are starting a new import into SLP with no existing stores, have you deleted the sl_id column from your export file?
Are you importing to the exact same WP site?
The CSV docs explains further about the CSV file headers and use of sl_id.
If you have already deleted the sl_id column, you didnt mention how large the import file is. If it is very large import your server may not be completing the import based on your configuration, limits , google query limits etc. etc. The Import is a 3 step process now.
If you have import messages on it will show you what your headers were and import info. See screenshot, I just imported a csv file of 86 locations that took less then 15 seconds and the import message file shows what was imported.