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If you look into the log files of Cryptomator, are there any error messages (WARN, ERROR or Exception)
Missing directory files due to incomplete sync. Cryptomator flattens the internal directory structure and uses linkfiles (dir.c9r) to keep track which directory is contained in which one. Some sync apps occasionaly miss to sync those files due to their small size, leading to missing directories. See also Security Architecture — Cryptomator 1.7.0 documentation.
If the dir.c9r files cannot be recovered, the directory becomes orphaned, such that you cannot access it anymore and all filenames inside the directory are lost. With the upcoming 1.6.0 version you’ll be able to reintegrate the directories into the filesystem hierarchy, but filenames & extensions cannot be recovered.