User blog comment:Xaero Dumort/Just announced: Mass Effect 3 : Retaliation/@comment-5362182-20121004182848/@comment-1679409-20121004183224

Possibilities:

1) The Reapers took many with them to dark space after the Prothean cycle.

2) The Reapers stored the Protheans' genetic code so they could make more.

3) There are more than one Collector base.

4) There were more than one Collector ship.