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I found a ton of small problems caused by non-existent lookup names. While fixing these I backed out the "remove" code. It now tries to deal with the problem. The user can now either a) change the lookup names and the invalid column values, or b) leave the bad data and hope for the best.
Another fixed problem: changing the "Show only categories and values available in the current library" threw away all edits. It is no longer possible to change that check box once edits have been done.
There are probably edge cases in how the UI handles correcting the bad data. In particular, undo doesn't work in the case where an invalid lookup name was changed to a valid one.
The changes are in calibre source.
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