You can make a backup of your customized file/table anywhere you want. Just copy and save. To upload the backup to the new version, you just have to upload your customized file/table where you have to make the customization. Just copy your customized file from the backup and paste it into the new version. (You have to paste customized files/tables into the same place of the new version where you have copied them from the old version) 

For example: If you have a customized index.html file in the current version. Now you want to update your application version. Copy and save the customized file (index.html) somewhere else(This is how you can make a backup). Now update the version. After that, copy the backup file and replace it with the index.html file of the new version. 

That's it.