Hi Bastien,
My guess is there might be some JS issue which is not loading the shortcode content.
Since you are anyways upgrading it to the latest it is not worth the effort to debug and find the issue.
Anyways, you can follow below steps to “export” all the shortcode data as a backup.
1) Deactivate the plugin
2) Go to plugin editor –> shortcoder –> shortcoder.php
3) Paste below line at number 172
echo '<textarea>' . esc_textarea( json_encode(get_option('shortcoder_data')) ) . '</textarea>';
4) Save the file
5) Activate the plugin
6) Go to Settings –> Shortoder
7) You will find a textbox with a text at the top. Copy that text and save that to a local text file.
Thats it. You can then remove that code which u added and save the file.
It is not necessary to backup since even after upgrade the old data will still reside in the DB for safety purposes.
Thanks,
Aakash