Just ran into this issue while testing out the linked boats in 1.12.0 (for Minecraft 1.11.2); had a few regular boats connected together, changed them over to chest boats, re-linked them, within about 5 minutes the chest boats had become invisible and would no longer move. Tried re-logging/reloading but without success. The invisible boats could not be destroyed (even in creative) though I could see where it was supposed to be thanks to the HWYLA HUD.