I will jump in as to how I would address this. Endnote has an option, but I guess it doesn’t achieve what you want though. Under the “sections” um, section of the output style settings, it lets you create a bibliography for each section, and to continue numbering or disambiguation etc etc (see image) OR create a bibliography for each section and a complete bibliography at the end of the document, but I don’t think one can be numbered in order of appearance and the other alphabetical.
Hence, if you stick with the section only option, after finishing up the manuscript and citations, you should gain a temporary group in the endnote program, which you can select and copy into a permanent group. Then you can export the group into a new document (RTF format to maintain font info) with a different -alphabetically organized style and paste it at the end of your document.
Not sure why you want the by appearance chapter bibliographies at the end of the document followed by the alpha version? but you can make a running appearance bibliography and then still generate the alpha list as described above.