Missing index entries

I have been working on a massive index (about 20,000 entries) on a ID CS6 document, a 700 page biological work of reference where all taxon names should be indexed. Took me several weeks. I produced the InDesign file from a Word file, but entered the index entries in InDesign (there weren't any in the Word file).
Now I found that many of my entries seem to have gone missing. They do not appear in the generated index. On the page where I entered it, the normal code (a ':' above a '^') is changed in a single ':'. I fear the last code, ':', means something like 'invalid marker', because they also appeared in another (crashed) CS6 document where they represented corrupted MS Word cross references (see "Cross references from a Word file", a still unanswered question on this forum). Normally when you select an index marker, the entry is highlighted in the Index Window. When I select the ':', nothing happens.
In the beginning of the book, I just marked any singular taxon name, but as it appeared that some taxon names appeared quite often, I started using the 'Add all' button in the index entry window. (I hope I use the right English names, they appear in Dutch for me.) This meant that some taxon names on earlier pages got double markers, but I thought that was no problem because the same markers on the same page only result in one entry in the generated index file. Could this be the bug that's biting me? I haven't found the problem in the later pages of the book.
A lot of the entries still found their way to the generated index, but of course I find this very worrying. Because I still have to process many author corrrections, I will have to generate the index again.
So, I have the following urgent questions:
-     Why does this problem occur, under which circumstances? Will regenerating the index result in more loss of entries?
-     Can those ':' markers corrupt my file in any way? What are they? (With the "cross reference problem", after some time I was unable to open the file again, which would with this project give me a major problem.)
-     Can I somehow 'revive' the missing entries automatically? Or is there at least a way to search for the ':' markers? (They are hardly visible.)
-     How can I prevent this from happening in the future?

Forum participants are not Adobe employees. We're users like you who volunteer to share what we know.
Thanks for the added details.
Usually someone somewhere in the forum's global audience is awake and eager to participate at almost any hour. However, "super storm" Sandy in the USA has caused massive losses of power, transportation, and communication, so responses may be delayed for some time.
HTH
Regards,
Peter
Peter Gold
KnowHow ProServices
Fritschy wrote:
Thanks for your compliments, although they don't bring me any further.
The version is 8.0.1, I always update when I'm prompted to do so by the update centre. As far as I know it is an international version.
Still, I would guess the InDesign developers could tell me something about that ':' marker. I suppose the software didn't invent it itself.

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