The issue with items disappearing from chests does not appear to have been fully resolved in the latest version (v1.05) for Win64.
After saving and loading with numerous items in chests and nets, and many gardens and tree plantations, all items disappeared from chests and nets, all fully-grown trees and crops vanished, and all cans in water purifiers disappeared. In addition, animations glitched. All spear animations worked fine, but the fishing pole was the only other thing that showed up. The fishing pole's default position had the bobber hanging over the screen. Other than those two, every animation for every other equippable displayed as an empty hand looking like it was holding an invisible spear. Furthermore, the axe was unable to harvest trees, though it could break placed items as normal, albeit without any animation.
This continued until I saved and reloaded, whereupon everything went back to normal. I built my raft up substantially afterwards, but kept the number of items in chests low and regularly cleared out my nets, and the issue has not reoccurred. I suspect that the issue was a result of too many items in the nets, chests, and water. Multiple times I was able to go behind my raft and dive down to get coconuts that were floating in the water (at one point more than half an hour after I had last harvested a tree), so it's possible that not all coconuts that fall into the water disappear when they should.