In case anyone else using the i62HD has had this problem I will post the work-arounds that I found.
My original problem was that when using the i62 to read academic PDFs on the 6 inch screen I found that using landscape view and page scrolling was the most convenient for viewing the documents. Unfortunately, I have found that annotations made in scrolling mode do not show up in the new PDF file created through the MERGE function, though you can export them into a text file. Likewise, annotations made while viewing the PDF in reflow mode (the 200%, 250% font size, etc.) also do not show up when you merge the document. (And when they do show up, it's a big vague patch covering half of the page, not necessarily the sentence you originally highlighted). In the above post, Pooh suggested trying to merge using the old PDF reader. It was a good idea but it didn't work. The merged document was still blank.
Through trial and error I found that annotations made in page view will show up on a merged document. So the bug only occurs with annotations made in scrolling mode. On the 9 inch screen of the M92 this bug probably never shows up because the entire page can be read and annotated in page mode and navigating to the next page is simple. On the i62's smaller screen, however, reading a book in page mode is not easy, especially in landscape view. In particular, I found that if you use your fingers to navigate to the bottom of a page in landscape view and then clicked next page turn, it would take you to the bottom of the next page, not the top. So, reading in scroll mode or reflow is almost a necessity.
1. PDF reflow
I found that this works. When reading in PDF reflow mode I make a highlight and then change the view to 100% view (which shows the entire page). Then I tap my highlight again (so the window pops up allowing me to edit the content of my note). It is not necessary to type anything. I just exit that screen by hitting the home button and then go back to my prefered zoom level and resume reading. I find that as long as you tap each annotation in 100% zoom mode, they will show up when you merge the document. Alternatively, when you find something you want to highlight you can just go to 100% zoom first and then highlight the sentence but sometimes it can be hard to see on the 6 inch screen at 100% zoom.
2. Landscape mode and using page scrolling
Again, the easiest way is to read the document in scrolling mode and then open the menu and select 'Page View' just before you highlight something. After making your highlight you can open the menu and re-select scrolling mode to resume your reading. If the annotation toolbar at the bottom of the screen was sticky this would be much easier. As it is, changing page view means that you have to go back and bring up the annotation toolbar one more time, an extra step of clicks. Nevertheless, it is a small price to pay for merging my annotations.
In my case, at least, these work arounds have solved my problem of being unable to merge annotations in a new PDF file.
Hopefully the engineers at Onyx figure out the problem now that I have isolated it to scrolling mode and reflow mode but until then there is a way, it just requires a few more steps each time you make a highlight.