Referencing equations in/from appendix
In general, it is always easier if your cross-reference is relatively nearby—flipping between multiple parts of a text makes the whole thing harder to understand.

So I'd lean towards referencing the version in the appendix, all other things being equal. However, if you are referencing a whole series of equations in the main text, including one duplicated in the Appendix, then it would be OK to preserve the main-text reference.