You can not export data out of a FileMaker Go file and then import the data back into a FileMaker Go file because Filemaker Go can not export data in .fmp12 format and FileMaker go can only import data from a .fmp12 File. You will need to just import data from the old file into the updated file. This option is also easier to do. A trick that you can use to help you accomplish what you want is to delete a file on an iPad by exporting a zero found set of records with the file name of the file you want to delete.
Thanks for the advice.
Re importing data from the old file into the new file I have a slight problem here - I download the new file which replaces the old file as it has the same name, so there is no longer an old file to import from. I'm wondering if I can save a copy of the file to the FM Go temp location and import from there, or if you have any other suggestions about how to import from an old file into a new file that has the same name?
Rename the file that you download to something like update_file. Then run your import. After the import use the delete file trick to delete the old file. Use save a copy to make a copy of the update_file with the correct name for the file. Then delete the update_file. You should end up with a properly named new file with all of your data. These steps might take a little trouble shooting but I have been using this process to update thousands of fmgo files.
Since you are using a FileMaker server to get the new version from, I would consider sending the data from the "old" app to a table on the server and then get the new version and get the data to the "new" version from the server.
This is what we are doing, and we are not letting the user get the new version before the transaction sending the data to the server is done with success.