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I've seen this: https://infinityfree.net/support/why-are-my-files-deleted-after-uploading/, but to no help. Uploaded files are probably deleted for false malware detection.
I am trying to deploy a Blend4Web (https://www.blend4web.com/en/) application, all files < 10Mb etc., but the .html main file (the player with WebGL canvas) gets deleted after FTP upload.