rewrite permalinks for canonicals

How to rewrite permalink slug for canonical.

Have a custom setup for cpt /cpt-folder/%cpt-child-page%/%another-cpt-page%/

Right now canonical is not respecting the permalink rewrite:
/cpt-folder/%cpt-child-page%/%another-cpt-page%/ and become
/cpt-folder/%cpt-child-page%/%another-cpt-page%/%another-cpt-page%/

How can I rewrite and define the yoast canonical to listen to this rule as well? Without defining it manually on each page