Its true that Felipe didn't want Isabel Clara Eugenia to marry because she would leave Spain, but the main reason for Isabel to remain in Spain was because, engaged since she was 10 years old to her cousin, the mad Emperor Rudolph II, the marriage would never take place because Rudolph didn't want to marry.
In 1597 iFelipe, fed up of his nephew's indecision, resolved that Isabel would marry another of his nephews, cardinal Albrecht of Austria. Felipe wasn't able to see his eldest daughter married, as the wedding was celebrated in April 1599, months after Felipe's death.
These are Felipe's daughters by Isabel:
Isabel Clara Eugenia (1566-1633), by Sánchez Coello ^
and Catalina Micaela (1567-1597), by Sofonisba Anguisciola