Faced a situation where I was told that file was lost. It took 3 months for staff to find it they said it was in some other office records. So maybe its possible. Secondly, I was told if car was bought through the bank, file would be with bank!
Listen to @basitali87 advice. Any sort of records/papers problem in any car old or new is whole headache, you must visit Lahore ETO office and keep at least 2 days for there. Go early by 8am max to avoid rush.
By the way, why you told agent to return to you book and money? Even if file is not found, ask him to give you original computerized book. Make some deal with him as he has your documents now. You have to be patient, no other choice.
As far as name showed on MTMIS, my dear sometimes you will be surprised when the act is caught without proper documentation, name goes back to previous owner! Be very careful!
Last, there is no "one" record room. Files are spread in various rooms, various buildings, various locations.