Do not deactivate the module. Module's deactivation has nothing to do with upgrade. It removes the module from your WHMCS and permanently deletes its data from database. To undo this operation you'll need to restore from backup.
Do not upload new files in fancy ways. We've seen customers uploading files one by one, directories in wrong paths and clicking "No" when FileZilla asks them to overwrite files. If you don't overwrite files you are keeping outdated versions thus the upgrade took place. here, select your module and click Manage button (requires login). You can see an example in the screenshot below.
Next page lets you download the latest version of the module giving you multiple download options depending on your PHP version. If you need help choosing the right package click here or Help me choosing visible from the screenshot below.
All downloads are safe. Files are verified multiple times per day automatically. For security reasons we won't share details.
That's it. You have successfully updated your module to latest version. If the module requires changes to database or in file structure it will perform all actions automatically.