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I found solution for above problems. most time this happen because cut dose not include dependant solid  so when hole sketch change it position (Either by I logic form/code or manually  change )  and  move on top of some other solid that are not previously selected as parent dependant and it show this ineffectiveness error.
This below video provide more detail how to fix this kind of issue just select all solids structure also edit features of hole so you can fix the issue. 

 

Also this online video help to set hole in different solid in design