In this case, you cannot update the valid length of your stay in Vietnam to 90 days with your new visa letter while you are in Vietnam under Visa exemption.

You have to leave Vietnam when the visa exemption period stamped on your passport ends, then use your 90 days Visa to re-enter.
Or you can apply for a new 90 days Visa while you are out of Vietnam, then re-enter, to be able to stay in Vietnam fully 90 days.

To ensure compliance with Vietnam's immigration regulations and safeguard your rights, you must present valid residence documents (such as an electronic visa) to immigration officers at the border. Additionally, carefully check the temporary residence certificate stamped in your passport and promptly notify immigration control at the border if any information is inaccurate.

Any queries, feel free to contact us at Visa@vietnam-evisa.org