Past simple or past perfect ?

Which one is more correct?

a) It is hard to say whether the more up-to-date file had indeed been on his desk before the meeting took place. If it had been he should be regarded as a liar.

b) It is hard to say whether the more up-to-date file was indeed on his desk before the meeting took place. If it was he should be regarded as a liar.

Thanks in advance