It depends what you are trying to fix, the server or the client.
Scenario 1 would work but it is the sort of thing you have to do when you have had a problem with the sync server. It will not avoid the time taken to transfer the data. In fact in this case you will be sending the data to the sync server. Most Internet connections are asymmetric and upload at a speed that is far far slower than they download. In my case the upload speed is a tenth of the download speed so an upload would take ten times longer. Also if you clear the data from the server you will clear the data from all clients. As you will have more than one client connected to the sync server you will have to sync the others again afterwards as well. If you have 3 clients, that's downloading 25,000 notes and their attachments three times.
Clearing the sync server is something you do not do unless you are certain that is where the problem is and you really, really have to.
I have never had to use it but the advanced option to re-upload the client data may avoid any impact on other connected clients but it will not avoid the need to upload everything.
If you think that you are having problems with a client and you want to reset it and start again the methods I mentioned in your other post will only affect the one client and, if you have asymmetric network speeds, the download will be faster.