I have just given an answer to a similar problem. Features:

• Shows how to use checksum files with controlled timestamps where necessary.
  • There, it's not .aux to .bbl but index files .nlo to .nls, but you get the idea.
• Alternatively recommends latexmk.
  • Shows how to use latexmk with automatic dependency tracking in a GNU Makefile.
  • Example configuration latexmkrc for custom makeindex files as used by the nomencl package.

Have fun.

There is an answer to a similar problem. Features:

• Shows how to use checksum files with controlled timestamps where necessary.
  • There, it's not .aux to .bbl but index files .nlo to .nls, but you get the idea.
• Alternatively recommends latexmk.
  • Shows how to use latexmk with automatic dependency tracking in a GNU Makefile.
  • Example configuration latexmkrc for custom makeindex files as used by the nomencl package.

Have fun.