I was trying to get a water source in my home, so I dug a trench from the nearby ocean. It went rather well, but I did run into a few issues involving cave entrances. Here’s what I gathered:
When a cave entrance appears, a formation of rocks appears underground like this, with X representing rock and O representing the cave entrance.
To plug a cave entrance up, you need to use soil, sand, etc. on top of both entrances, but you must block the aboveground entrance FIRST. If you try plugging the underground entrance first, it will not work. Additionally, you can’t plug up one side and then attempt to go through the other, as it will reveal the entrance on the concealed side again.
However, I had some issues with these cave entrances re-appearing while digging my trench. After many, many attempts, it seemed to work after I deepened the water, and changed the ground type from soil to sand. Not sure which of these did the trick, so further testing would be appreciated!
(I wanted to do a write-up on the wiki for this, but I think some more information first would be a better idea.)