Wordpress is installed in a subfolder with another install in the root. The subfolder requires root/index.php/page permalink structure

I have a group of wordpress sites. There is an install in the root that uses permalinks as expected, eg /%postname%/ = root/postname for the URL. In the subfolder installs that structure results in a 404 error, but if I structure the links to include /index.php/%postname%/ they work just fine. This just started happening today after having run fine for about two months.

Things I've done to try and get the subfolder sites working again:

Rewritten the htaccess,
Insured mod_rewrite was active
Deactivated all the plugins for the subfolder install
Tried various permalink structures (all result in 404)
Installed a backup from when it was working
Created new sites in subfolders and tested navigation with the same results
Deactivated Wordfence in the root install and all plugins in a cloned subfolder test site

On the same server I am able to create sites in a subfolder under a different URL whose permalink structure works as expected.

Has anyone experienced this or have suggestions on what to try next?

Solution

I was never able to fix this problem and moved the site into a subdomain where it is currently running fine.