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@manawydan - you won't like this suggestion, but... FWIW
There were some changes around the time calibre 1.0 was released that changed some things about file path/name lengths - they were shortened a bit. There have been a couple of instances of subsequent problems, including getting more than one file of the same type into a book folder. I'm wondering if your problems are another consequence of those changes - although the other problems were not calibre crashing.
My other thought is that 100,000 books seems to be quite large in the world of calibre libraries, I'm wondering if you've bumped into a practical limit on your configuration.
Calibre Portable will support multiple libraries. I think you said you had 100,000+ books. So create 11 similar libraries in the Calibre Portable folder (Library01-Library11). Add first 10,000 books into Library01, do some tests, if OK load second 10,000 books into Library02, repeat until done.
The Add is important as that will ensure the folder/file names conform to the current 'rules' under the post version 1.0 regime.
If you get to 100,000+ books in 11 libraries without any apparent problems then copy the books from the Library02 to Library01, do some tests; if OK then copy the books from the Library03 to Library01 repeat until done or not OK.
BR
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