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Hi,
There was long thread about this problem which is accessible at the link I posted below:
https://wordpress.org/support/topic/cant-edit-main-theme-php-files-after-upgrading-to-4-9/
I also encountered the same problem. But my problem was not related to the plugins. My problem is more related to loopback check. My configuration is the following. WP site’s wp-admin folder is protected with IP acls. I saw that when I’m trying to edit some file – it seems that WP site as a client is trying to access wp-admin folder and fails as this IP is not in IP access list for wp-admin folder. When I add IP in access list – I’m able to edit php files. I need some advises how to fix this problem without adding IP to IP access list.