Is Flonase working even if I must blow my nose after taking it?

Most likely. Intransal steroids such as Flonase are highly lipid soluble and have good tissue binding. That means the drug is delivered to the target cells quickly and efficiently. It is always a good idea to blow your nose before you administer the drug to maximize contact between the medication and the nose. Take your medication on a regular basis, even if you feel well. Flonase works best over time.
Probably. It penetrates deep into the nose and the sinuses and you will not completely eliminate it if you blow your nose afterwards but why not hold off if you can?