WordPress Rewrite Problem Solving _ Application Skills

A problem these days has been bothering me because my WordPress is placed in the root directory of the site, so I built some subdirectories to run some other apps, I found that these applications were disturbed by the rewriterule of WordPress's. htaccess file, and I had a great effort to modify. htaccess files so that the rewriterule of subdirectories can work properly, but found that the application of the call subdirectory always returns a 404 state, but the content is normal Of
In fact, if the establishment of a subdirectory playback Discuz forum, the forum Rewriterule will also be disturbed, the problem is really confusing, especially after the return of 404 states, all files will not be included in the search engine.
After some debugging and modification, I found a very strange way to solve this problem, is in the subdirectory of the PHP file to add the following line of code:
Header ("status:200 OK");
Then I use some HTTP status test tools, the directory and file will no longer return 404 status, but return to 200 status, and then I will look at the subdirectory in the search engine, it is expected to return to normal. Some of the features of WordPress are really strange, and I don't know why.