Using Pretty Permalinks causes redirection misdirection of main page

I’ve never had this problem with other hosts, but I am having a problem with a client’s site.

Background: He has 2 domains pointing to the same site; Domain A is original, Domain B is the current domain (A being redirected in some way to B)

Setup: I set up WordPress in a some directory of the main directory (which Domain B is pointing towards). Everything works perfectly.

Problem Situation:
After setting up WordPress Permalinks to Custom: %postname$
Now, when typing in the website address: https://www.maindomainB/WPsubdirectory, it redirects to https://www.maindomainA/WPsubdirectory.
When clicking on the links on the WordPress site, everything goes back to normal: https://www.maindomainB/WPsubdirectory/pagename.

Desired outcome yet unattainable:
1. Pretty Permalinks
2. Link to main WP site directed toward DomainB (not redirected to DomainA)

Troubleshooting:
Playing with htaccess file with no luck yet. Removing custom permalinks fixes it, but I no longer have nice permalinks.

Any way to create pretty permalinks directly or stop the incorrect redirect?

Please help!