I already hinted something about another restriction regarding aimless browsing. The lifespan of document marks depends on rather ill-defined and (for an average mortal) mostly non-deterministic technical conditions.
Generally, marks _always_ survive when not moving away from the document or when moving only in the session history (and unhistory). That means, if you go back and the "unback" to the document, you will find your marks safely in place. If you follow a link from the document (or typed an address to the Goto URL dialog) and then go back (by pressing the right arrow or through the File menu), your marks are safe too. These are in fact by far the most common usage cases for the marks, so most of the time it will just work as you expect. That's a good news.
The bad news is that in all other cases, nothing is guaranteed. It might work if you get back to the document by any other means (by following some link or typing its address to the Goto URL dialog), or it might not. It might be possible to achieve two instances of the document inside a single ELinks, each with its own set of marks. However, again, generally it will work as expected - this paragraph serves only as a disclaimer in cases it doesn't. Don't rely on it.
Marks never survive over ELinks restarts. If you quit your ELinks completely and run it again, the marks you placed will be no more. No exceptions. Well. In some cases, it might appear that they survived, but that just means you did not quit your ELinks _completely_ --- if you run multiple ELinks instances under a single user on a single system, they "join" together and you must quit (or kill) them all to get rid of the damn thing. But that's a different story.