To do it one marker at a time, without messing up the ones you haven't yet done, start with the last marker & work towards the beginning.
This assume that once you've done a cut, you no longer need the marker.
Consider replacing the sections with silence or with a low-level tone that will be easy to re-locate. When done go back and delete those sections.
To replace, highlight the section and choose Generate... Silence
This is a really general answer and you may get better ideas by chatting with someone in person but:
I think this is a really classical example of balancing time, effort and economics (how much are you asking for, how much are the others asking for). It's really just something that you need to balance, so that it feels good for you and others that are ...
Yes, this is possible. I've used MP3 Trimmer which does this. However, the result was unplayable in some programs (no audio after the first point in the file I edited), so I ended up reencoding anyway.
Yes there is. It's called a crossfade and is a very basic part of audio editing technique.
As a crossfade starts, you are playing two clips at the same time, however for the duration of the crossfade you are reducing the gain of one and increasing the gain of the other. At the point where the first clip is no longer audible, the second clip is at full gain....
Audacity is a classic, freely available, open source DAW that should work for recording lectures. When I record podcasts, I'll occasionally want to pause mid-recording to collect my thoughts or look at notes. I use the 'p' keyboard shortcut to toggle pausing and continuing recording.
Alternately, you could record the entire lecture, and then use the build-...