The easiest explanation would be that Tiber Septim died in 3E 38, while Mysterious Akavir (given its call to action against the Akaviri) may well have been written through information from the 3E 290 invasion (or even more recently, if it were based on the works of explorers). The snake-men could well have eaten the men of the continent in that time period, even if the process had not been started as of 3E 38.
That's not to say Mysterious Akavir should be taken without a grain of salt, given the jingoistic descriptions, internally anonymous author, and knowledge that a normal explorer or member of the 3E 290 invasion could have likely found out.
That's not to say Mysterious Akavir should be taken without a grain of salt, given the jingoistic descriptions, internally anonymous author, and knowledge that a normal explorer or member of the 3E 290 invasion could have likely found out.
Not to mention what is said about the information http://www.uesp.net/wiki/Lore%3a%50ocket_Guide_to_the_Empire,_3rd_Edition/Other_Lands.