-Rakata didn't die out, they were thought to have died out, but they survived underground while their feral brethren remained on land. They did lose their connection to the force, however, they used certain devices to make up for it. Except technology couldn't substitute for everything which is why they needed Revan to open the doors.
-HK-47 I don't know the exact lore on this guy, so I am most likely wrong BUT! in both KOTOR and KOTOR II you have to find parts to him, HK47 being blown up: in pieces or whatnot seems to be fairly common and he just keeps coming back. Being destroyed and rebuilt is completely normal regarding him. In fact it has happened many,many times.
- No idea on Cathar, but it's true they were on the verge of extinction however they rebuilt their homeworld and restored it to its full glory.