So im reading infernal city, it says that red mountain erupted once more and then the argonians raided in retaliation for their years of slavery resulting in the slaughter of the dunmer, forcing the few remaining dunmer to scatter, or reside in soulstheim. when did this happen? are the books canon?

This mean that morrowind will have been destroyed in the release of skyrim?

Not to be rude, but we have a LOT of threads on this. There's one on the front page I'm pretty sure. The search bar will answer your questions.

Happened sometime after the Oblivion Crisis, and the argonian invasion was sometime after the Red Year and 20 years before the Infernal City. And yes, the books are canon.

Also, Morrowind isn't completely destroyed. Vvardenfell was covered in a few feet of ash, with the seas around it still boiling 40ish years after Red Mountain erupted, yeah, but the island is still there. Doubt the mainland had any significant damage, save for likely ash falls and some tsunamis along the coastal areas south of Vivec city.

Also, the argonians only really hold contested land in southern Morrowind to be part of Black Marsh, with the rest of Morrowind likely patrolled by wandering bands, or something.