Must the seller of damaged wheat and barley bags (which were received three years ago) be compensated, knowing that he was late in retrieving them within the agreed-upon period?

These bags were a trust (amanah) with you, and a trustee (amin) is not liable without transgression (ta'addi) or negligence (tafrit). Therefore, if you did not transgress against them and were not negligent in preserving them, then you are not obliged to return their equivalent or their value to him.