Thanks. I'll check your ideas.
So far, after wasting a lot of time I have figured out that up to 4,064 links in toc.ncx files work fine. Between 4,065 and 4,080 links gives as many warnings (Warning(index build): string too long (max=255). Truncated.); however, the resulting mobi file actually includes all the links. 4,081 and more links in toc.ncx gives only two of the above warnings and does not include any toc.ncx links/waypoints into the resulting mobi file.
I feel (I don't know programming) that there is some connection to some variable in the code (unsigned integer on some systems is 0 to 255). I don't know if there is a data type that has 4,064 limitation
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