I do post regular updates in the support channel on discord and yes the issue did appear again but we are closer then before.
As I finally was able to reproduce the issue I could find out what was causing it. Our chunk loader plugin caused this issue but only when there was a chunk loader placed which explains why the issue only occurred after a while. I did remove the plugin now and opened the server again without any rollback needed. I don't know what exactly is causing the issue in the plugin yet. We will look into this further and check if it's an issue in the plugin or sponge, once we resolved the issue I will readd the plugin. The fail save script will stay active just in case and it doesn't cause any issues anyways.
I'm not sure if this bit of info is any help, but, sometimes multi block structures can cause world corruption. One time back on 1.6.4 one of my maps got corrupted after I broke an active Tinker's Constructs smeltery which caused an instant crash and my map was rendered unusable until I used MC-Edit to remove all traces of the smeltery. Worked fine after that.
Well, doesn't that seem a bit irrelevant? That was 1.6.4, and this is 1.12.2. [doublepost=1523286040][/doublepost](Not trying to sound rude, but still, 1.6.4 =/= 1.12.2)
sometimes, old solutions might work to new problems too. or at least might give an idea of an aproach.