Importing does not “remove stores” There is a function under locations bulk actions called delete permanently.
You should make sure you have a back up of your site.
You can export your locations download to a csv file. (Some docs, about large exports configuration etc and export to csv file)
You can them delete. You do not show us your plugin environment so I do not know if you have the Power add-on. You need the Power add-on to export/import
You can make changes and under the import function choose how to handle duplicate . Review the notes on the sl_id column. You should not use that header on reimports unless you are using exact same sl_id in the locations datainfo)
here is the documentation about Duplicate handling.