The game removes files in the following cases:
- On download error in the DLC get. This can only remove the files that are marked as DLC in our database though, and there currently isn't any DLC (the one that's in the game is "on-disc".)
- You reset your mappacks. This will only delete "smb" and "portal" mappacks.
- The case above where it deletes the following folders:
"dlc_a_portal_tribute", "dlc_acid_trip", "dlc_escape_the_lab", "dlc_scienceandstuff", "dlc_smb2J", "dlc_the_untitled_game"
Thus, it's impossible that it was the game that deleted your mappack.