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When something loses its reference it will ask for a new one when you edit the definition of a part in the assembly. I am getting very frustrated when I have to correct a model and like you seee in the picture below, the component placement tool refuses to pick up any surface. It picks up all lines and if I am not looking directly at the hole (i.e the model is turn sideways or I am "looking" at the hole through other components) the tool will pick up the inner surface for the constraint. Does anyone know what causes this?
I am not sure what Creo's logic is for picking features. It doesn't seem to consider proximity of the cursor in all cases but rather follows a type, which is not always logical to the task at hand.
When I have a bad reference, I go to the assembly placement dialog and delete the offending relation and, since it is now highlighted, go to pick the feature I want to place the error with. I find that using the filters (lower right of the window) helps target what I need.
You should use the "Query Select" and turn off the preselection highlighting, that way you pick EXACTLY what you want. I think a lot of people's problems are that they don't really know what references they're actually picking, and are getting bad ones.