If any exe's in the NetSim gets deleted due to Kaspersky antivirus here are some steps to add NetSim exe's as an exception in Kaspersky Application without disabling the Antivirus protection.

Step 1: Open Kaspersky Window, Click on Settings as shown in the figure:

Step 2: Click on Additional

Step 3: Click on  Threats and Exclusions

Step 4: Click on Manage Exclusion

Step 5: Click on Add

Step 6: In the "File or Folder" text box browse to <NetSim_Install_Directory>/bin or copy and paste the bin path of your NetSim Directory which will be like "C:\Program Files\NetSim\ Acad_v12_1\bin" (In lower versions of NetSim, "C:\Program Files\NetSim Academic\bin) 

To get the path of NetSim bin path easily just right click on NetSim Shortcut on Desktop click on "Open File Location", copy paste the path to this "File or Folder" text field.

Step 7: Click on Add, press Continue if any prompt displays

Step 8: Now click on "Specify Trusted Application" next to Manage Exclusion

Step 9: Click on Add button

Step 10: Click on Browse 

Step 11: Go to NetSim bin folder and select NetSimSimulation.exe

Step 12: Click on Open

Step 13: Check several checkboxes as shown in the figure and then click on Add. Close Kaspersky.

Note: If Kaspersky has previously removed the NetSimSimulation.exe, then it might not be possible for you to "Specify Trusted Applications", as explained in Step 8 onwards. To restore NetSimSimulation.exe, you could reinstall NetSim either silently to save time or manually as per your convenience.

Additional References: How to Perform Silent Installation of NetSim?