I teach an adult Bible study class, and I use Logos for all of my notes and highlights. Your question touches on one of my specific concerns, because they use a proprietary format for their datasets. The best solution I have is that I export the notes and format them in Markdown, and I distribute them to the class via one of my blogs. Obviously, I can't include verbatim copies or quotes from the sources I use, but it's better than leaving the notes inside a platform that could (potentially) disappear in 20 years.
I cite all sources used in the footnotes of every session, so at the very least, it should be possible (theoretically) to obtain the source material in printed form and find the exact page number (Logos stores page number metadata in the digital copies). It's probably not ideal, but it's the best thing I've come up with so far that doesn't require a lot of duplication of effort.