JOEL - They are not lost. From what I understand they did take the Nauvoo temple ordinance records with them but I am not sure where the originals are kept (perhaps the Church Historical Department keeps them in the granite vault in Salt Lake City?). The records are available on microfilm through the Family History Library in Salt Lake City on the "Nauvoo Temple Endowment Register". You can probably access them at any local LDS Family History Center as well.

The following site lists the names and dates on the Endowment Register:
http://www.xmission.com/~research/family/familypage.htm

There is also a seven volume set of books that has the records of over 15,000 baptisms that were done in the Nauvoo temple. Information about this is at the folowing site:
http://familyhistory.byu.edu/nauvoo.asp

An article about early temple ordinance work is at the following:
Baptisms for the Dead—A Forgotten Record For Finding Early LDS Ancestry