I work for an Apple Authorised Service Center, and standard operating procedure for us with parts is the following:
1. Diagnose the fault
2. Order a replacement part
3. Install replacement part
4. Test to ensure fault is corrected.
Diagnosing the fault could take anywhere from 1-48 hours depending on the number of machines in the queue. Ordering the part means that it should be delivered within 24 hours, but depending on the time of diagnosis could be as long as 48 (or longer if Apple don't have it in stock). Installation should happen on the same day as part delivery, but again this depends on the queue.
I would say that something like a fan replacement should take 2-3 days if the service center is not working in overload.
No respectable service tech would delete your data without contacting you first to ensure you have a backup. If your data is important, you should have made a backup anyway.
In my honest opinion, a fan replacement shouldn't cause a tech to have to wipe your hard drive, unless there is some software fault that is causing the problem to begin with.