A lot depends on the setup of the two current multisites:
- Do they share a common user base, if any?
- What kind of plugins are installed, if any?
- Likewise themes?
- Is it obvious which one is going to be imported in to the other?
- How many different authors are there? Things like author IDs will possibly have to be synchronised?
- What about user comments?
The reason for all these questions is that at the base of it, each site will have it’s on wp_X tables. So merging the databases won’t necessarily be so difficult, although obviously one set of database will need to be renamed. Then you’d need to update the wp_blogs table accordingly.
But once you start thinking about all the above questions it has the potential to get really messy and I am not sure if automating it is possible (or if worth the effort for 40 sites compared to doing it manually as you suggested).
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