I started writing a simple tool a couple of days ago for just this task: merging two Arduino Hex-files into one.
If you are brave enough to try some beta-software, please go ahead here: https://github.com/tobiasvogel/hexMerger
The latest released version can always be found under "Release" at the top of the page.
Please be aware that I just started this project, so there may be bugs, or it even may not work at all under certain circumstances.
Leave a comment or feedback and I will be happy to review it and improve the tool as far as I can!