Most of the time, the expression “Je vous en prie” is an answer when you ask something. It is used mostly after a question beginning by the “pouvoir” verb which means “can“.

For exemple :

• Puis-je prendre du chocolat ? / Can I take some chocolate ?

• Je vous en prie

So in your case, this is exactly what it means : like a more polite way to say “OK“.

You can also use “Je vous en prie” when you let someone do something. The most common example is on the public transport. When you see an old person and you want to let him/her sit, you would say : “Asseyez-vous, je vous en prie / Please, take a seat“. The use of “Je vous en prie” here let the old person know that it doesn’t bother you (and that is quite polite).