Both "did not" and "had not" appear to be plausible verb tenses. Let's start with a)
a) Please do not deduct My loss of pay as I did not bring my attendance card.
- "deduct My loss of pay" does not sound correct. "deduct" and "loss" may be redundant such that one of them could be removed.
- the second part of the sentence would be clearer if the time/day were provided.
Intermediate attempt at the sentence:
c) Please do not deduct my pay, as I did not bring my attendance card on Wednesday.
However, strictly speaking, I think "deduct my pay" is not correct either. "reduce my pay/paycheck" is another option.
Next, another rewording:
d) Please do not deduct any money from my paycheck on Wednesday. I had forgotten my attendance card.
Next, a total rewrite just for fun:
I wish to apologize, on Wednesday at work I forgot to bring my attendance card. Please do not deduct any pay for that day, since I was present. You may confirm that with (name of co-worker or manager).
So, d) and e) may be interesting answers.