This bug still occurs in 1.16.200. I have a trading hall with all the villagers stuck in individual spaces and a max level farmer somehow changed into a max level cleric. I did not remove his work station. The only thing I did was move some brewing stands to switch villagers on another part of the trading hall.
After testing a bit, on a server and a realm, mining ore blocks that do not drop themselves naturally (i.e. nether quartz, diamond ore) and crops including nether wart all have a chance to reappear regardless of unbreaking status, so having unbreaking 1-3 would be the same when mining these blocks as when it is absent from a tool. Moreover, this can also happen in these ore blocks even if the player is using a vanilla, unenchanted tool. This does not appear to be a problem in offline play. Additionally, planting crops in rapid succession also causes the crop to disappear at random while still being in the player's inventory (this applies to nether wart as well).
It seems to have gotten worse in 1.16.100 and even worse in 1.16.200 since I had an autosorting room that prior my PC could easily run at 144fps. 1.16.100 arrived and it was down to about 100-110fps, and 1.16.200 I was around 70fps.