As you will hear TIME and AGAIN.
PDF is a terrible source.
Was that original chapter title box an IMAGE? it could
land anywhere on the page during conversion.
Since you know codeview. Look in the Images grouping of the file browser. are your
missing titles there? Then the above applis and all you need to do is find the code and move it to where it VISUALLY belongs
FWIW I had a similar issue when I firs came upon Calibre - MR. I learned (fast)