It's unadvisable to delete any countries from your database. Doing so DOES prevent ANY use of those removed countries for anything, including registration and sales and shipping quotes.

It's better to "disable" certain countries via your Admin. Deleting them altogether is generally a bad idea.


And, now that you've deleted them, you'll need to put them back by completely wiping out all the tables related to countries/zones, and put back the originals that came with Zen Cart: countries, zones, geo_zones, zones_to_geo_zones.
And, if you've ever added any countries/zones back via your Admin after having deleted some, you're going to run into some issues with your historical data that utilized those incorrectly-added records.