Obstacles seen by planning but not expected by AMCL

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I am not sure how to formulate this question. Our robot has a hand made map of a space. We use fiducials to orient it on that map and use AMCL to maintain localization. Then we use move base etc to navigate to another area.

If we put an obstacle on our map (say a "no-go area") but there is not physical obstacle there, this will confuse AMCL.

How would we define a "no go area" that is not physical so that path planning avoids it, but AMCL is not bothered by the absence of something physical?