Sorry for the late response! If you don't get a reply within a few days or a week, it's totally fine to bump the topic. Unfortunately I also tend to lose track of the Java sections of the forum (this isn't your fault, it's my fault, restructuring the forum is still on my to-do list).
However, unfortunately the log files only cover the most recent and previous game session, so they are only helpful immediately after such a problem occurs. Ideally send a report from the game right when you notice that something is missing or weird, this will automatically attach the log files. It's basically the only way to find out what's really happening.
There is a bug that objects and plants sometimes don't get loaded properly on clientside, but this is typically fixed by reloading the chunk (either by moving away or by reloading the world). Losing objects permanently for no reason is that seems to happen extremely rarely... if someone ran into such an issue before, it was typically related to "Gravity", i.e the objects did break because they had no contact to the ground.
However, recently I found a bug that caused gravity to break objects in rare cases, even if they had contact to the ground or something solid (originally this issue was raised in connection with blueprints). This might be responsible for the objects to disappear in your case.
I've also expanded the logging to the "Events.db", so whenever an object is deleted, it will be tracked. When sending a report after the next update, a dump of this file will be attached automatically (this should make it easier to find out why a particular object disappeared).
But as a quick fix in the meantime, you can turn off Gravity for objects (and plants) in the game settings. That should prevent objects from breaking.