Moving from subdomain to top level, link/image paths incorrect after manual edit
Is this Drupal 7 or 8? Not sure that it matters, but take a look at around line 102 of your .htaccess file, should look like this:

# Modify the RewriteBase if you are using Drupal in a subdirectory or in a
# VirtualDocumentRoot and the rewrite rules are not working properly.
# For example if your site is at http://example.com/drupal uncomment and
# modify the following line:
# RewriteBase /drupal


The issue you describes sounds like the RewriteBase is incorrect. What does your .htaccess say?

Can you also tell me what your settings.php file has for the base URL value?

# $base_url = 'http://www.example.com';  // NO trailing slash!