Is it really necessary to place the appendices in a book in the order in which they are referred to, or is it possible to have a "logical" order, i.e. place them in an order which would be chosen when the Appendix would stand alone? For example, Appendix G referres to another appendix, which logically would be placed as Appendix H, but because the reference appears so late, that appendix would end up as Appendix Q when placing the appendices in the order of references.
I would have no problem putting appendices in "logical" order. An appendix is referred to out-of-context or out of order anyway, so what difference does it make if your footnote sends the reader to Appendix A, Q, or IV?