The problem in your file is not necessarily related to its size or the number of hyperlinks. Something else may have been implemented in a complex or non-standard way.
If you want to make changes to the file to make it usable, the first thing you'll need to do is remove the DRM. We cannot tell you here how to do that, but Apprentice Alf can; google for his blog.
Are you using Calibre? If so, there is a simple trick that often helps to make an unruly epub behave: load the file (without DRM) in Calibre and convert it from epub to epub.
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