If I would not use BoxCryptor and would delete a file on windows in the BoxCrypor directory it would be moved into the Recycle Bin where I it usually stays for a very long time.
Using BoxCryptor seems to delete a file permanently which is risky. If I work without internet connection (e.g. in a plane) then I can't continue working till we land and I can access it from the could storage. But I might be busy then and forget about this and for example MS Skydrive only guarantees to keep deleted files for 3 days (Skydrive didn't even have a way to restore deleted files till Sept last year).
It would just be way better if I could simply get it from the Recycle Bin and continue working. If you are worried about security you could move the encrypted file into the recycle bin.