In the LVS report, I found there were missing instances layout. After checking the source netlist, I found those missing instances were empty subckt in my cdl netlist. Meanwhile, layout cells with same cell name were found in layout but not in layout netlist. There was no devices in that layout. (metal, poly, nw, with pins on some of the wires./not all the wires) Those cells seemed got flattened into top level that caused the mismatch. I used "preserved cell", but not working. Only way to make it work right now is black box those cells. I have concern of using black box. Is there any another solution for that issue?