aristotle - 8:36 pm on Nov 21, 2012 (gmt 0)
Your idea to "Write to Google for a re-inclusion in the index?" may be premature. You need to investigate the problem in more detail first. For example, have you checked to see if you've gotten any messages about a penalty in Webmaster Tools? Also, have you confirmed that these sites were actually de-indexed, or was the loss of traffic due to rankings drops?
From the information you've provided, it would be difficult for anyone to identify the specific cause of the problem.