Concatenating all the files into one sort-of works but when I replaced biblatex' \printbibliography[heading=none] at the end of each file with \newrefsection[biliographyfile] in the combined file, the reference sections become empty.
Now I can make the chapter title the top level header in each file and then put \newrefsection just after it and insert \printbibliography at the end and the includes work with proper bibliography. Now the tikz issue remains to be resolved. I'd love it if "#+TITLE: chapter title" automatically became a section and everything under that turned into subsections at proper depths though.
Thanks, Subhasis