Apparently you didn't bother to read my entire post. I did delete all the .PK3 files in ETMAIN, and then I reinstalled the game, so that all the base .PK3 files were restored. Including PAK0.pk3.
What I included was the error message from the ET starter, which examines all the files in ETMAIN. It indicates that there were a huge number of files in .PK3 files, but it certainly doesn't show ALL the .pkf3 files as there were 470 .PK3 Files containing 3,640,597,317 bytes.