A few days ago WP pushed an update. This update has been known to break a lot of plugins shortcodes incorrectly. When you said:
I’ve tried disabling all plugins (Over then the plugins needed)
The only way to be sure is to deactivate all other plugins. They should not be needed in during the file upload process.
I’d like to test on my test server, but I don’t know how large .pdo files are, I’ve never dealt with them. If there is such a thing as a “small” .pdo file, can you try uploading it here so that I have something to test the upload with?
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