I have a website on WordPress ***.com and I also have a subdirectory ***.com/partners
This subdirectory has its own backend and it’s like a different website, is there a way to migrate the website with the main domain name without touching this subdirectory at all?
If you are talking about using Webflow hosting (required for CMS) then not without front ending Webflow with a reverse proxy server to route /partners traffic to another host where the app was hosted on a subdomain. You could also pull it off with Cloudflare Workers. Either way you introduce a new point of failure and overhead. Personally I would just put the app on a subdomain, and create a redirect to it on Webflow.
You mean the new app right?
Yes. app = new app (/partners)