Is Cloudron using a correct/full path when issuing the cp over ssh? I've had this problem, too, and I know I'm not spanning ZFS pools. If we enter a root path into the config, should't Cloudron use the full paths, for correctness/completeness/clarity, when issuing the cp?
I don't think that helps much, but I've seen the same persistent issues that @dummyzam is pointing to.