Updating STEAMCMD screws the install by deleting files? :/

So after I ran app_update 4020 validate on steamcmd…
files from the settings/ folder and resource/ folders went missing.
I received the “FAILED TO LOAD FROM FILE resource/ModEvents.res” and player_auth @ line 72 (users.txt)
I’m scared to run the update again now,
Files form cfg/ are also missing.

http://forum.facepunch.com/showthread.php?t=1250283