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I'm no expert, but I've had my index "issues" over the years. I think anyone wanting to help you will want to know whether you've tried using the Binary Index setting in the Project Settings.
We have projects with much bigger HHK files than yours, so that's not the problem.
Have you opened up the HHK file in Notepad (or other text editor) and taken a look?
We had the type of problem you described when we imported topics from a different project and those topics had keywords saved in them (instead of in that project's HHK file. This was caused by a bug in RH X5.
If you did that, I can give you the workaround we used. (Sorry if the formatting below isn't ideal -- I'm just going to paste the whole thing in from a different source.)
Warning: It is time-consuming if there are many keywords to fix.
1. With the project closed, have someone with MS Access open its .cpd file and print out KKeywordList. From this printout you can see which keywords are causing the problem, because the problem-causing keywords have a negative value.
2. Delete the .cpd file.
3. Make a backup copy of rhkkeyword.apj.
4. Using Notepad, open rhkkeyword.apj and add the problem keywords manually in this format:
Multi-level keywords are inserted as follows:
<name>first level keyword</name>
Warning: The <keywords/> tag occurs only once for each main keyword, and it occurs after the last subkeyword, if any, as shown above.
5. Save and close rhkkeyword.apj.
6. Reopen the project and click the Index tab. If RoboHelp fails to open or crashes, then you know there are syntax errors in rhkkeyword.apj. Delete the .cpd file, fix rhkkeyword.apj and try again.
7. When RH's index is displaying properly, check for any subkeywords whose main keywords are not defined. (These appear bolded.) For example, if you have "batching\grouping" but not "batching", add "batching" to a topic.
8. Recompile help and check it carefully.
Hope this helps.