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I am currently writing a thesis in which a lot of derivations are moved to the appendix. To make these derivations readable, I sometimes write sentences like "As we saw in equation X...", where equation X is present both in the main text as well as in the appendix.

My question: should I, while writing the appendix, reference the instance of the equation in the main text, or the one in the appendix?

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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.

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I would reference the appendix number in the appendix so as not to break the flow, but you might also footnote a cross-reference to the place where it appeared in the main text if it helps remind the reader.

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My approach is usually to write something like

"... and we arrive at

(A3) E=mc^2

as in equation (42) of the main text. Now, substituting for m in (A3) we obtain..."

etc.

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