Problems migrating - still links to old system

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I developed a site in v8.2.1 and am now trying to migrate it to a new URL/folder but am having great problems.

I developed the new site as old-url.co.uk in a folder /old-folder, using database olddb and then wanted it replicating under a new URL, new-url.co.uk in a new folder /new-folder, with database newdb. All this is on the same server.

On the old site I turned off all caching and emptied /application/files/cache and I copied the contents of /old-folder (with permissions) into /new-folder.

I created a new database, newdb, exported olddb and imported it into newdb and I modified /application/config/database.php with the new database details.

There may have been a few other odds and ends but when I went to new-url.co.uk the site showed up correctly however a lot of links were pointing to old-url.co.uk. These included the link from the logo and all the top level navigation items ans well as SOME of the lower level nav. items.

When I hover over the links I see that 'incorrect' ones include index.php while 'correct' ones do not, i.e. a wrong link will show old-url.co.uk/index.php/topic while a correct one shows new-url.co.uk/topic.

Furthermore, if I go to new-url.co.uk/login and login I end up at old-url.co.uk/index.php/dashboard/welcome and I am then connected to the old database!

Looking at the sql of the database I exported and imported, there is no sign of old-url.co.uk in any of the tables other than logs

Can anyone shed any light as to what is going on, what I can do to fix it or what I did wrong and can re-do correctly? I thought I'd followed all the documented instructions.

There is some stuff in .htaccess but removing it doesn't make any difference. Just for completeness, it contains
<IfModule mod_rewrite.c>
   RewriteEngine On
RewriteCond %{SERVER_PORT} 80 
RewriteCond %{REQUEST_URI} !^/[0-9]+\..+\.cpaneldcv$
RewriteCond %{REQUEST_URI} !^/\.well-known/pki-validation/[A-F0-9]{32}\.txt(?:\ Comodo\ DCV)?$
RewriteRule ^(.*)$ https://www.bird-control-company.co.uk/$1 [R,L]
   RewriteBase /
   RewriteCond %{REQUEST_FILENAME} !-f
   RewriteCond %{REQUEST_FILENAME}/index.html !-f
   RewriteCond %{REQUEST_FILENAME}/index.php !-f
RewriteCond %{REQUEST_URI} !^/[0-9]+\..+\.cpaneldcv$
RewriteCond %{REQUEST_URI} !^/\.well-known/pki-validation/[A-F0-9]{32}\.txt(?:\ Comodo\ DCV)?$
   RewriteRule . index.php [L]
</IfModule>

where new-url.co.uk is actuallyhttps://www.bird-control-company.co.uk...