Currently, the only way to detect a deletion is by running CyprtSync in the background.
It would be great if CryptSync could (optionally) detect deletions happened before it started, and in the "sync and exit" mode (perhaps by using a(n optional) database like many other file sync tools do).
Details:
I am syncing some of my personal folders between two computers using CryptSync+Dropbox, and it's a two way sync. Both CryptSync and Dropbox start on boot, and normally there's no problem with deletion detection because CryptSync is faster.
However, occasionally, my Windows could get hiccups and certain programs wouldn't start on boot even when they're supposed to, or I might turn off "start with Windows" for CryptSync for some reason (e.g. accident or testing) and forget to turn it back on. Turning on CryptSync after Dropbox finished its syncing could mess up both my decrypted local folder and encrypted Dropbox folder without detecting deletion.
There might be concerns for the safety of filename encryption with such a database (although its content could also be encrypted), but for people not using filename encryption (like me), this would be a great option to have. Furthermore, such a database could also detect file movement and save some work for CPU and disk.