Once you paid, the agent should issue the ticket straight away and if he hasn't then it is perfectly reasonable to hassle him to issue it

I would also be going in and sitting down and insisting that he fixes the class of service and make sure it is business class before leaving - or if he doesn't , getting the money back

nothing wrong with being excited

Maybe he still waiting for when he can upgrade my ticket using his miles coz I heard you cannot just do ut right away you still need to wait when it is available. Well goodluck to him I wish he would be able to do that before my flight.

The main point is that he shouldn't be upgrading using his miles. That means he charged you more for an economy class ticket.
This procedure is not allowed. Travel agents have to book the class of service you requested.

There is a chance that the upgrade seats never become available (if he is actually doing this) and you will have to travel in economy when he charged you extra for an economy ticket.

if that is what he is trying to do then he is issuing a ticket in breach of EK's terms and you could just find yourself paying out EUR2000 and being denied boarding

If you have paid him for a business class ticket , then he must issue a ticket properly in business class

As I said, you need to go in and get him to properly rebook you in business class ( that is O,I,C or J ) and get the ticket issued

Alternatively get the money back and rebook elsewhere and I would be writing to Emirates to detail the nature of what the agent is doing

If he was able to do so is it possible to upgrade all my flights to business? ( 4 flight in total ) or he can only upgrade 1 flight per book? Like let say the flight from larnaca to dubai?

he cannot legitinately ( under airline rules ) use miles to sell an upgrade at all ( if that is what he is doing ) .

You have paid him for a business class ticket, get a proper business class ticket from him

It is possible, but as Dave Noble and I have been trying to tell you, it is against Emirates terms and conditions to do so, and if they find out, they will cancel your ticket, and you will be denied boarding without a refund.
You should find out exactly what he is doing, and if he isn't booking you an actual business class ticket, cancel and book somewhere else.
I would report him to EK as well, as he might be ripping many other people off too.

This whole thread sounds really dodgy to me...

yep.

I agree, there is something very wrong going on.

It did make me wonder if a travel agent with enough regular customers who are not aware of FF schemes could sign his customers up and retain control of their online miles accounts.

It is up to you, but I would trust what EK says about the ticket over what someone claiming to be another customer of the travel agent says

There is something decidedly fishy about what is going on ; it's your EUR2000 but I think you are taking unnecessary risks with your trip

Get the exact precise details of what the agent is doing and then check whether this is permitted by the airline.

on the manage my booking section of the EK website it will state the ticket class ie chose your seat.

All my bookings allow me to select my seat and it is all in the class of travel I booked ie in Business it is business class seats or in First it is first class seats.

This has happened in the past along with agents who buy miles on the open market, even cases of outright fraud at the airport have all made the papers.

Either way a pretty big risk even if you get on the plane that you might expect a tap on the shoulder in Manila or more likely Dubai.