The allowable settlement criteria is based on utility of structure. For examples, in Process and Oil & Gas industry, piles supporting structures that have pipes are normally limited to 6mm vertical deflection. This value of 6mm is also considered by Pipe Stress engineering when they are doing their pipe design and in this way the design comes to full circle. Differential settlement is also considered.
If you are asking for a building, the it depends on what values your building columns can tolerate considering differential settlement and not fail. Piles undergo short term and long term settlement in clay soils. You should evaluate both based on the recommendations of geotechnical engineer and see how the values affect your superstructure.
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