You have a lot of files that are reported as empty by the underlying file system. Where is you vault located? Maybe some fancy non-standard filesystem?
The errors reported can not be fixed automatically. A lot of the ciphertext files are reported to be empty. Sanitizer can not guess what should be the correct contents.
It is expected that you have more ciphertext files than cleartext files. This is due to the fact that also directories and symlinks end up as files and for every file with a very long name there will be an additional file inside the m directory.
It is indeed possible some files are now missing. Neither is it possible to show files in the directory listing, for which the corresponding .lng file in the m dir is empty, nor are empty ciphertext files shown.
To solve this, you need to find out, why that many files are empty.
The problem for me is that there are over 60 000 documents/files from way back until today.
It’s hard to notice some files disappearing.
The reason I tried the sanitizer is a lot of warnings from cryptomator:
12:57:08.412 [Thread-86213] WARN o.c.cryptofs.CryptoDirectoryStream - /home/kfo/grive/Dokumenter_enc/d/DE/5MFL6WUIJFQPKBRGEAEU65CQVRE36Q/THV4VVDOQ6ACEY7IDTQG2RMQRLTGT2D4.lng could not be inflated.
12:57:08.465 [Thread-91613] WARN o.c.cryptofs.CryptoDirectoryStream - /home/kfo/grive/Dokumenter_enc/d/AF/DL3AJYYVYBH42O2KLTZV3JNM5BJ24S/DE33P45PMCXLW2NXL6FUXRJ5VFOTYAB4.lng could not be inflated.
12:57:08.465 [Thread-86213] WARN o.c.cryptofs.CryptoDirectoryStream - /home/kfo/grive/Dokumenter_enc/d/AF/DL3AJYYVYBH42O2KLTZV3JNM5BJ24S/DE33P45PMCXLW2NXL6FUXRJ5VFOTYAB4.lng could not be inflated.
Yes, it is a problem. It doesn’t have any negative effect on your other files, therefore it is just a warning during directory listing. But as your sanitizer check result confirms, (not just) a lot of your .lng files are empty.
Search for DE33P45PMCXLW2NXL6FUXRJ5VFOTYAB4.lng inside your m directory. Can you confirm that this is a 0 byte file?