The copyright owner may release a work under two or more different, and perhaps incompatible, licenses, if s/he so chooses. The owner may release a base work under one license and a derivative under another.
One obvious risk is that a user might be able to get and re-use the key elements of the work under the less restrictive license (here the CC-BY license) and so the restrictions of the more restrictive license would have no effect.
Here another possible issue is that since the final paper "must be under CC-BY-NC-ND by publisher's rules", the publisher might take the position that you have in effect released nearly the same paper under a broader license, and that this is an attempt to evade or violate those rules. The publisher might call that breach of contract and sue you, or might just refuse to publish your paper at all. That would be up to the publisher, and would depend on the details of your agreement with the publisher.
But there is nothing illegal or even very unusual in having released the same content under two different license as far as the world in general goes.