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I believe I have encountered a spelling dictionary bug.

If you accidentally tell Nisus Writer to learn a spelling, it’s impossible to unlearn it for the document in which it was learned.

Within the document, select the word and use the contextual menu to unlearn it.
Open any other document and type the word. It will now be flagged.
Return to original document and conduct a spell check. The word will NOT be flagged.

As you already know, there is a way to unlearn a previously learned spelling word:

1. Select the word in your document.
2. Right-click the word to show the contextual menu.
3. Choose the command "Unlearn Spelling".

You'll see the same "Unlearn" command in the Language palette and main menu Edit > Spelling.

That said, if you (perhaps accidentally) invoked the "Ignore Spelling" command, that would ignore the word in a particular document for the duration that document window remains open. If you close and reopen the document you should see the unlearned word is again flagged as misspelled. That may explain the behavior you encountered.

Please let us know if you continue to have trouble.