Is the below sentence construction is correct?
Do you remember, last time we had prepared one file for our work?
Or Simple past tense will do
Do you remember, last time we prepared one file for our work?
You have to use Past Simple because you are talking about an event that ended in the past and has no effect in the present time. You only want to know whether that person has any recollection of what you did (in this case prepared).
One more thing. You don't have to use a comma after remember.
Our boss rejected the file we had prepared. The rejection comes after the preparation, to make that clear you use past perfect. In your first example you use "the last time" which requires past simple, like last week for instance.