When using the linked controller on a lectern, if you break the lectern holding the controller being used, you will no longer be able to use any controller on a lectern in that world again, even if you go to a different dimension or relog. It does only affect the world it happened in, but it is reproduceable.

I figured to write this here since the issue is still open and this is related, but while I can confirm the 0.3.2b update now prevents this bug from being reproduceable, meaning no new worlds have to deal with this problem anymore, old worlds that were affected by the bug still can't use linked controllers on lecterns. Only old worlds affected by the bug, not sure about old worlds that didn't have the bug be produced.

You should be able to use lectern controllers again in the old world by dying.

Can confirm that worked, thanks! I'll close the issue now that it is fixed.
(Good thing it wasn't hardcore mode.)