http://the100.wikia.com/wiki/Echoes
In the episode 4x01, in the minute 28:42, in one of the monitors used by Raven, when she explains the nuclear threat to Monty, Jasper and Harper, there is a message where says "Contact lost with Asteroid Mining Penal Colony".
Probably there was a riot in the prision, the prisioners took the control, few time after of this came the Prainfaya and the people of the Ark forgot about the prision. The prisioners and his descendants (the prison must had modules for men and woman or they couldn't survive for 100 years) got to be self-suficient like the people of the Ark.
For obvious reasons after the riot they probably din't have any interest in have contact with the Earth or the Ark. When the first generation of prisioners died, maybe in some point they decided to find out why they were isolated in an asteroid, and they found the Ark...with Raven, Bellamy and the others inside. Probably they were captured and this is the reason because Clarke can't contact with them.
The communications in the bunker seems broken right after of Bellamy contacting with his sister, it's obvious they don't have anyone like Raven to fix it.