I assume you are using an isolated file rather than being connected to the server and want to update that files records. If you are instead using a remote connection, the updating is automatic as you are using the records on the server.
You can script the 'sync' or data transfer to work from Filemaker Go, not very difficult.
For newly added records, you would do a search and then an update script.
The difficult part is record serial numbers but that is easily resolved. You will have to add to your tables and scripts for this.
GoZync is a possible answer.
I was thinking of Filemaker Server conncted to filemaker Go on iPhones and iPads over wireless. I was concerned since FIlemaker go is such a new product, would the server be able to handle problems like loss of wireless connectivity half way thru an update. Ex. if data from 3 tables on the iPhone was sent, but only one of these tables on the server was updated before the wireless connection was lost, what would the server do?
The server only does what it is told to do, like all software. Well, I've written some that acted independently but that is a different story.
I'd refer you to the Filemaker Server forum for more specific info and also check out http://www.seedcode.com/gozync/ for a product that claims to handle it all for you. You can even ask them questions.
The issue you question is something akin to what happens to the records still unsent or sent and not flushed... There you would simply verify each record after the reconnect, something like that.