Each paragraph of content has a paragraph ID. A highlight is stored in the database with a start point (paragraph ID and word offset) and and end point (paragraph ID and word offset). The word offset is calculated by counting the words in the paragraph. For example, in "I, Nephi, having been ᵃborn of ᵇgoodly ᶜparents," [Nephi] is word 2, and [born] is word 5. Supposing that the verse is paragraph 1, and I wanted to highlight [Nephi ... born], the highlight would be stored in the database as starting at paragraph 1, word 2, and ending at paragraph 1, word 5. This is how Gospel Library for iOS, Android, and Windows have calculated word offsets for several years, and the new experience on LDS.org follows the same pattern.
The old experience on LDS.org, on the other hand, had a bug where it would count the words differently depending on whether or not the footnotes were visible (it counted footnote letters as their own words). For example, if footnotes were visible: "I, Nephi, having been ᵃborn of ᵇgoodly ᶜparents," – the old experience considered [Nephi] to be word 2, and [born] to be word 6. So the highlight was stored in the database as being from words 2 through 6, instead of words 2 through 5. This would cause problems when syncing with Gospel Library, because if you created a highlight on the online study tools, it would be misaligned in Gospel Library, and vice versa.
All highlights created in Gospel Library the past several years are "correct," and all highlights created in the old experience at LDS.org are "incorrect." However, looking at the database where highlights are stored, there's no way to know which highlights were created in Gospel Library and which ones were created in the old experience. Furthermore, it's impossible to know which ones may have already been corrected by the user. Therefore, there's no way to fix old experience highlights without causing all of the other highlights (which were created in Gospel Library) to suddenly become misaligned in the other direction.
Because the old study experience at LDS.org was not maintained very well, it caused permanent problems for users' annotations. I'm glad that we're finally at a point where it will soon be retired in favor of a new experience that aligns with the other platforms. And I hope that the next time there's a similar bug, it will be caught and fixed before it becomes a permanent problem.
I know that doesn't fix your misaligned highlights, but I hope the explanation helps you understand why it can't easily be fixed.
Samuel Bradshaw • If you desire to serve God, you are called to the work.