I did some testing concerning a problem with highlights and annotations. From some of the posts in this thread it seems that the disappearance of highlights are restricted to kepub files. But since not every post clarifies the file type I am not sure about that. In any case, I did my tests with kepub.epub files.
The results suggests that highlights that do not get displayed at the screen are related to TOC links that contain a fragment identifier (e.g. <content src="text/part0002.htm#phasellus" />).
If you go to a passage via a link that contains a fragment identifier and then highlight it, you can see the highlight at a later time only if you go there by the same link. The same is true if you go to a page via this link and page forward or backward to a passage and highlight it then. However, if by paging you cross a page that contains a TOC link without fragment identifier (or maybe any TOC link?), and set then the highlight, the highlight will be displayed irrespective of how you get there.
I did the testing on KT under FW 2.3.1. I attach the file and put the description of the test into the spoiler. The TOC file contains four links, only one, Section C, contains a fragment identifier. If you would like to reproduce the test, it might be important for some points of the test that you select the font size in such a way that the heading of Section C is somewhere in the middle of the screen page, and (important for only one point of the test) that the begin of the last paragraph of Section B is not at the same page as the heading of Section C. I selected Georgia and put the size slider a little to the left of the middle position.
See
this post on how to repair not appearing highlights/annotations.
Spoiler:
action: open the TOC and select "Section C"
action: highlight "Phasellus"
action: highlight "rhoncus"
action: go to annotation list, open the menu next to "Phasellus", then select Show on Page
result: correct page, no highlights
---
action: highlight "dignissim"
action: go to annotation list, open the menu next to "dignissim", then select Show on Page
result: correct page, "dignissim" is highlighted
---
action: open the TOC, select "Section C";
result: "Phasselus", "rhoncus" and "dignissim" are highlighted
---
action: open the TOC, select "Section B"
action: page to "Section C"
result: only "dignissim" is highlighted
---
action: open the TOC, select "Section B"
action: page to "Section C"
action: highlight "tincidunt"
action: go to annotation list, open the menu next to "tincidunt", then select Show on Page
result: correct page, "dignissim" and "tincidunt" are highlighted
---
action: open the TOC, select "Section C"
action: highlight "Donec sodales" (Last but one sentence of Section B)
action: open the TOC, select "Section B"
action: page to the end of "Section B"
result: "Donec sodales" is not highlighted
---
action: open the TOC, select "Section C"
result: "Donec sodales" is highlighted
note: In the annotation list, "Donec sodales" is listed under SECTION C
---
action: open the TOC, select "Section B"
action: page to the end of "Section B"
action: highlight "In dignissim quam" (last sentence of Section B)
action: open the TOC, select "Section B"
action: page to the end of "Section B"
result: "In dignissim quam" is highlighted
note: In the annotation list, "In dignissim quam" is listed under SECTION C
---
action: open the TOC, select "Section B"
action: page to the end of "Section B"
action: highlight "Nulla mi" (third last sentence of Section B)
action: open the annotation list
result: "Nulla mi", "Donec sodales", "In dignissim quam", and "Phasellus" !! are listed under SECTION B, the other passages under SECTION C.
----
action: open the TOC, select "Section C"
action: page to the beginning of "Section D"
action: highlight "Praesent"
action: open the TOC, select "Section D"
result: "Praesent" is highlighted
----
action: open the TOC, select "Section C"
action: page backward to the beginning of the last paragraph of "Section B"
action: highlight "Praesent enim turnis"
action: open the TOC, select "Section B", page forward to "Praesent enim turnis"
result: "Praesent enim turnis" is not highlighted
note: "Praesent enim turnis" is listed under SECTION B
---
action: open the TOC, select "Section C"
action: page backward to the end of "Section A"
action: highlight "Fusce molestie" (last sentence of Section A)
action: go to annotation list, open the menu next to "Fusce molestie", then select Show on
Page
result: correct page, "Fusce molestie" is highlighted