There are tow possible causes: Either something deleted the files or your vault got partially corrupted.
To check the first case:
If your vault is synced with a cloud, see if your cloud provider offers a file history. With this file history you may be able to restore encrypted deleted files by remembering at what time you deleted them. Once you have synced the changes, all deleted files should be where they are supposed to be. Because Cryptomator encrypts the directory hierachy and the file names, you need to restore all files in the targeted time range.
For the second case:
Look at the log files and see if there WARN or ERROR messages. They may indicate corruption (like a lost directory link or something). You can send us your log files by uploading it somewhere (i suggest Firefox Send) and send me a PM. For corrupted directories, we have the sanitizer tool.