We have two internal Crowd directories and users cannot change their password in the second directory. Is there any chance to change the password by a user in more than one directories?
No, sorry. Crowd operates by authenticating the user via the first directory in which they exist; if they exist in two directories, they won't ever be authenticated via the second directory, and so theoretically* the functionality to reset their password in the second directory won't ever be used.
Worrying about multiple passwords per account would also be confusing to users (even more so than say Google's application specific passwords which are surfaced with 2 factor auth).
* I said theoretically earlier because you're probably asking about this out of more than plain curiosity. You could implement a standalone "password reset" application (using Crowd's REST APIs which authenticate as a newly configured application in Crowd which only has that second directory mapped) if you really wanted to go down this path.
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