Please note that we have had two different versions of the NET Bible, Version 1 and Version 2 as they have come from the authors of the NET Bible.
In OUR version 1 of the NET Bible, the purchased product was in two files, a NET Bible file (NET.ontx) and a NET Commentary File (NET.CMTX).
When OUR version 2 of the NET Bible was produced, because we had to remake the module from scratch, the set up was changed. Since the notes were not that involved or that many, the notes were made in the actual Bible file as footnotes.
To view the NET Bible notes in version 2
Open the NET Bible version 2, click in the Bibleview window, and toggle the footnotes with a simple ‘F’ key. Note that the notes didn’t change textually between Version 1 and Version 2. The people who wrote the NET Bible didn’t change their notes or add to them.
If you have already purchased the NET Bible version 1, and you install the NET Bible version 2, then that installation will overwrite the net.ontx file, but IT WILL NOT DELETE THE NET 1 COMMENTARY FILE. So, please, manually delete the NET 1 Commentary file, and use the footnote feature to view the notes in the NET Bible version 2.
If you look at the NET version 2 Bible and the NET version 1 commentary file, you might see an upgrade to version 2 warning. To fix this, delete the NET 1 Commentary file, and use the F key in the Bibleview window to view the notes.