James
All flanges should be modelled as a rigid using the valve/flange database. This defines the flange element as a rigid length and weight.
The flange check box in the input is for if you wish to check the loading on a particular flange using either the equivalent pressure method or some other method that i cant remember off the top of my head . You can then use this to see which flanges may need further investigation to see if you have potential leakage issues.
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Thanks
Adam