Here’s what seems to have worked for me:
I installed the “String Locator” WP plugin and did a search for the word “shortcode” in all my plugins. I found out that the plugin that needed fixing for me was Bootstrap for Contact Form 7.
Using my FTP client, I opened all the files of the plugin that needed fixing (i.e. those files where I needed to replace wpcf7_add_shortcode() with wpcf7_add_form_tag() and etc.) with Notepad++. I then used Notepad++’s Replace All in All Opened Documents (Ctrl+H on your keyboard) to replace all the deprecated stuff.
I then saved and reuploaded the edited files using my FTP client.
Hope this helps.