Why did Uthman (may Allah be pleased with him) request the parchments (ruqaa') to copy the Mushaf, despite the availability of Hafsa's Mushaf? Does this indicate that Zayd ibn Thabit did not compile the entire Qur'an in Abu Bakr's Mushaf, or was Uthman's purpose to compare and verify?

The reason for the compilation of the Qur'an during the era of Uthman (may Allah be pleased with him) was the disagreement among Muslims regarding its recitation. Hudhayfah ibn al-Yaman suggested compiling the Qur'an, so a committee of companions undertook the task of copying the Mushaf of Abu Bakr al-Siddiq (may Allah be pleased with him) into several copies, writing down what they differed on in the dialect of Quraysh, and burning all other copies. The companions unanimously agreed on the correctness of this action, and the copied Mus'hafs were sent to the Islamic metropolises along with reciters.

As for the narrations that indicate Uthman (may Allah be pleased with him) collected the Qur'an from parchments, this was for the sake of confirmation and precaution, not doubt. They indicate that he collected the Mus'hafs and compared them with what Abu Bakr (may Allah be pleased with him) had collected and with the parchments he possessed, integrating the review of all these sources during the copying process.

As for the statement of Ibn Umar (may Allah be pleased with both of them) that much of the Qur'an has gone, the intention behind it is what was abrogated in recitation from the Qur'an, not that anything of it was lost. Scholars confirm that what is present between the two covers of the Mushaf today is the complete Qur'an, and whatever was omitted was due to abrogation, or lack of continuous transmission, or not being part of the final review.