Blank files being deleted automatically after upload in htdocs

It seems likely to me that the file manager is discarding the empty files. If they are empty, they have no data, so there is no reason to have them, right? Of course, that’s not always true, it’s possible that your website might need them as placeholders. It might be possible to work around that through the website code. But regardless, if you upload them through FTP instead, that should allow you to upload all files as is without them getting deleted.