Just so we understand you are referring to moving files/folders that are encrypted and inside a Vault?
After you create a vault for your encrypted files you should not manipulate what is stored inside the vault using File Explorer from outside the vault.
I always hate to bring up this subject but is there any chance your data was backed up prior to messing with it?
It is especially important to be vigilant with doing backups of your encrypted data with the vault closed.
You should treat the root folder of the Vault as a hidden system folder that you never ever touch.
Everything in the vault was put there by Cryptomator and it needs to be treated like app data.
If you want or need to move files and folders that are in the encrypted vault you should Mount the vault and then move the files and folders using the drive letter of the unencrypted data.
Never mess with the encrypted folder structure. Treat the encrypted folder tree as part of the software. Hands off.
Directory id reused means, that two directory link files point to the same directory. For you this means “opening” two different directories leads to the same directory.
files are no longer visible
Reused directory ids normally does not make single files invisible, only directories disappear.
Before any fix, ensure that the vault is synced completely and offline available. Your vault is messed up. In order to repair it, the folder names will be lost.
Make a backup of your vault
Disable any sync software.
Delete the parent folders of the dir.c9r files from the message. If the message says
Directory ID reused: c155a57b-688b-4a4d-8b79-7fbdd4bc58fb found
in C:\Users\Doobie\myVault\d\RT\6AQD5Y4CCVXXXOE3D3IZOX3KEDSA44\r69zeocbIDcndumFXnMYzpfGC8URsfi2.c9r\dir.c9r
and C:\Users\Doobie\myVault\d\RT\6AQD5Y4CCVXXXOE3D3IZOX3KEDSA44\kODuJd7ohr_gZS8vrqzNS7tYlg==.c9r\dir.c9r
Then delete folder r69zeocbIDcndumFXnMYzpfGC8URsfi2.c9r and kODuJd7ohr_gZS8vrqzNS7tYlg==.c9r.
Rerun the health check
Fix any orphan directories messages
Close health check
Unlock vault
Inside the unlocked vault, browse through the LOST+FOUND folder. The formerly disappeared folders are shown there, but only with default names, since folder names cannot be recovered.