I am updating this thread because the steps to reproduce the bug no longer work. I think ink in general is affected by a large number of bugs, so it's difficult to cleanly separate them into different threads.
As of the September 18th bugfixes, many methods of obtaining ink can only create 'used' cups of ink. As far as I can tell, a successful 'full' cup of ink can be poured into an inkwell and change the description, and it seems to be able to be used to write more than just a few lines (so the initial bug reproduction method in this thread no longer applies).
However, if a bugged used cup of ink (I use this description to refer to a cup of ink that is obtained from a method that should produce a full cup of ink, but the cup is instead used; I think 'natural' used cups of ink exist in the game but I don't have a reliable way to obtain one) is poured into an inkwell, one of two things can happen.
In the first scenario, the description of the inkwell does not change (if it was empty, it will stay empty). An empty inkwell filled with a bugged used ink cup can be used to write 1-2 lines, and then will be truly empty. Considering these bugged used cups can also only be used to write a similar amount of lines, I think this behavior is actually not bugged, though perhaps the description should not say that they are empty when they contain a miniscule amount of ink.
In the second scenario, the inkwell removes itself from the game (it no longer shows up on inspect or right click). I have only tried this with an inkwell on a counter. Before September 18th, two of my deleted inkwells reappeared within a few days, and they both reappeared completely empty despite having an apparently full cup of ink poured into them. However, no further inkwells have reappeared for me. I think I have two missing inkwells due to this bug, but I could be misremembering; according to my logs, there is at least one missing inkwell that was witnessed by a different player.
I can't think of something that differentiated the inkwells that disappeared.