From our Knowledge Base:
"BoxCryptor uses two keys for file encryption: a master key which is derived from a user supplied password and a volume key. All files are encrypted with a volume key which is generated when a new encrypted directory is created. The volume key is stored encrypted by the master key in a configuration file (.encfs6.xml) at the top level of the source directory. When BoxCryptor mounts an encrypted directory you have to enter the password. The password is used to derive the master key and the master key is used to decrypt the volume key which is then used for file encryption."
To answer your question: When you change the passwords, the files do not have to be re-encrypted. Only the volume key has to be re-encrypted and the configuration file to be updated. That's it.
Hope I could help you!