From my point of view there are only three things critical for encryption (4 with 1.6.x and newer):
- your Masterkey file, which has to be stored in the vault root folder (App version 1.5.x)
- you password (or token or whatever will be possible with 1.6.x)
- the vault structure. Means: do not touch the d folder or the subfolders. If you rename the d folder, nothing can be decrypted anymore. If you rename/move subfolders, the files within cannot be decrypted anymore.
Only for Version 1.6.x: your vault.cryptomator file, which will identify your vault. Without that file, the app will not recognize your encrypted files as a vault.
But, as @NLS already said: each file is treated separately. If a file or a bunch of files get corrupted for whatever reason, all other files will be fine.
PS: if you are afraid of data loss (everyone should be), do your backups