Keeping fancy URLs displayed

For some reason (yes I’m crazy, I had to do custom changes to run a multilingual WP 😉 ) I had to turn off the usual pretty permalinks option on this site. We in fact generate our own “pretty” links, which a custom htaccess rule then rewrites.
WordPress apparently handles URLs perfectly, which it receives in the “standard” form of fqdn/p=?123. All links work fine, but my issue is that for articles links inside the page they remain in their “pretty” form of /lang/id/keywords-here/ whereas for links in the header menu, URLs in the navbar do end up as fqdn/p=?123 and I need them to remain as they ware in the original source link. The only difference I see is that menu links are from pages, and articles in the contents are about just that, articles. So how does WP handle that “internal” rewriting ?
Help appreciated !
Regards.