There's nothing difficult about it, apart from the ***** ache. 
You have to import all the topics into one project, fix all the links, rework the TOC, index and glossary etc. Getting the idea?
It seems odd to create a project with just five topics unless there is a very good reason. Are you sure you are familiar enough with what you have inherited to be entirely sure your predecessor didn't have some reason.
3,000 topics in one project should be OK but try to avoid too many in any one folder. If you also have lots of images then test things as you go. I have had more than 3,000 topics in a project but I have also seen people have issues with a smaller number but a high number of images (into four figures).
Perhaps do it in stages still having a merge but with fewer projects, see how that goes for a while and then amalgamate more.
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