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I found something informative in the Amazon docs.
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Yeah, makes sense that it uses a fuzzy algorithm. That was solved by removing the ë in the orth value
After more testing I'm encountering more issues.
Apparently, some inflections don't get picked up in some words, whereas an inflection with the same form of another word gets picked up.
For example, the word капли can be both an inflection of ка́пнуть and ка́пля, but in my kindle only ка́пнуть gets picked up, and it makes no sense because in both cases it's just an iform, not even the orth. I tried deleting orth values but it change nothing.
The order in the xhtml files can't explain it, as ка́пнуть (picked up) is 06 6696 (xhtml, line) and ка́пля (not picked up) is 01 7778.
The same happens for example with есть. It's a form of быть and есть, and even removing orth values doesn't change only есть being picked up, and есть (picked up) comes later in the files, 00 955, whereas быть (not picked up) is 00 113.
Guess I'm yet again stuck.