Hi,
One can't "delete" imported transport request and "deleting" transport request will not undo changes to development objects. Once you have verified via transport logs that the transport with the program was indeed imported into production system, there are two likely choices:
1) either there was other transport that deleted the program and it was subsequently restored under other transport, which is not yet imported to production; or
2) if the urgent repairs are enabled in production, it might also have been deleted directly in production
To check 1) use transaction SE03 to find the transports which contain the program. To check the 2) use SE38 in production system to access version history of the deleted program. I believe, the repairs do produce a version management entry.
cheers
Janis