when an encrypted file is not shown in the BoxCryptor drive, this might be caused by either a non-matching encryption key or - if filename encryption is enabled - a loss of filename capitalization.
If you have filename encryption enabled and the filename capitalization is lost (e.g. the filename changed from "DjUEu0" to "djueu0") the filename cannot be decrypted anymore and thus the file is not shown. Solutions for this problem are to restore the previous filename or by creating a "dummy" file (create a new empty file with the desired filename, copy the encrypted new filename, delete the dummy file and replace the "broken" filename with the copied one).
The other reason could be the loss of the encryption key. BoxCryptor stores all required information for en-/decryption - secured by your password - in a configuration file named .encfs6.xml which is located in the root of your encrypted folder.
If this file is lost or overwritten, the required key for decryption is lost and decrypting the files is not possible anymore. Overwriting this file can happen if you try to mount an encrypted folder with BoxCryptor on another computer before the whole encrypted folder has been synced completely. If the .encfs6.xml configuration file has not been synced yet, BoxCryptor does not know that this is already an encrypted folder and asks you to create a new password - which is then used to secure a newly generated configuration file.
If this happens, your BoxCryptor drive will appear empty, because the encryption key does not match anymore and the encrypted filenames cannot be decrypted. The only solution for this problem is to restore the original .encfs6.xml configuration file. If this is not possible, the files cannot be decryted anymore.
Most synchronization services like Dropbox allow you to restore previous versions of files, but unfortunately Windows Live Mesh does not seem to offer this feature. Could you restore the .encfs6.xml file from a previous backup you made yourself?