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It may cause issues, or maybe not. I have a set of stairs artificially blocked on the map and it causes no issue. I'm sure the more you move away from reality the more risk there is.

You should try it and see how it goes. If issues, you can use one map for AMCL and one map for Move_base. That should avoid the issue and allow you to mark up the no-go zones as much as you want. See the answers to my question here:

https://answers.ros.org/question/294462/nav-stack-one-map-for-amcl-and-one-for-move_base/

DISCLAIMER: I have yet to implement the two map system. It's on my list.