It's not a simple process and even when you get it all working you have to consider issues such as when two different users modify the same record and then sync the data back to the main copy of your file.
I recommend investigating two third party produced tools for synching your data. One is offered by SeedCode and the other by 360Works.
I think you are absolutely right ... there are lots of nuances to be treated when we talk about data replication.
But what I was thinking is to sync in 1-way (iPad => Server) only the transaction added during the period off-line.
Can I copy somehow one record from a table to another table in another file?
Import Records can move data from table to table and this is generally the method used to synch your data. It can even use an 'update matching' option to match an id number in the record to an id number in a record in the target table so that the record is update with data from the source table record with the same id number.
THis can be done at a time while you have a solid wiFi or other link to your server and can be from a remote location such as an office or coffee shop with wiFi.