If this happened to you like it did to me don’t assume – like I did – that WP Engine’s clone tool does a search and replace on your database to update the URL too.
Instead, when I spoke to WP Engine support they suggested it had to be done as a separate step.
Me: I thought that would happen as part of the clone process
Me: So next time we do a clone we should do a manual search and replace in the database too?
WP Engine Support: Correct.
WP Engine Support: Or jump on chat and we can help.
I still feel like this should happen automatically – maybe I was just unlucky on this occasion – but if it happens to you you can do a search and replace via the Advanced menu, if you have it available, in the WP Engine admin under the install you’re trying to fix.
To do this, use the wp search-replace command in WP-CLI, e.g.
wp search-replace urloforiginalsite.com newinstallurl.wpengine.com
Otherwise just ask WP Engine support and they’ll do it for you.