If there are modified files in the store, an information will appear.
In order to upload the update, you must restore the original package files.
https://shop.example.com/update.php/installerweb/list
A list of versions of this package available for download will appear.
Copy the files in binary transfer mode.
Another solution is to delete the modified files from the FTP server (to create a backup copy, copy the files from the server to the local disk) and upload the update. The system will upload the latest files from the package in place of the deleted files during the update process.