Desktop client deleted files after migration to new server

I planned to migrate to a new server. Some months ago I copied all the data from the old server to the new which had a temporary adress. I wanted to try it out with all the data I had at that moment. I finally decided to migrate and changed the DNS so that it points to the new server.
The new server was not synchronised with the data that had been added since the temporary copy. I assumed that the desktop clients would synchronise the added data to the new server after the migration.
Unfortunately the desktop clients removed all files that had been added, so I now miss 5 months of data. I have now stopped all desktop clients from synchronising, and happend to have some computers which had not been opened and I can save most of the old data from them. I could also access the old server from the IP-number.
My question:

  1. Was I wrong to think that the desktop clients would update the new server by synchronising their data thaat was missing on the new server? Is the synchronisation not 2-ways?
  2. How can I update the state of data in the new server to the most recent? Do I have to import the data directly to the new server? Or can I add the data to the desktop clients once again?
  3. At what point can I restart the desktop clients? Can I trust that they will synchronise new data that is added either to the server directly or to the clients?
  4. Is there something wrong with the configuration of the clients or the server?

The server is assumed to be the master unless you take extra steps[1][2].

Many thanks for very useful information

I realise we did not follow these instructions. I do not know how the repointing of the DNS was done, but the original server was definitely not stopped.
The problem is that I have not full access to the new server. I have stopped the old server.
Now that the accident has happened, what can I do?

I think that the new server was setup 5 months ago as a copy of the old and it seemed to work OK. So it had a similar setup as the old. However since then there has been som upgrades and the new is now running NC27 and the old NC26.

For the moment all clients that I know about have been stopped. I have saved most of the data. What can I now do to best repopulate the new server with the added data?
I am not sure if I have rights to run commans on the new server (we wanted a managed server as I will leave the responsibility of runningthe server itself).

But for the future - will new files that are added to the clients folders be synchronised to the server? I am confused…