If you are having problems with Incremental Deployments and the error message is “The changeToken refers to a time before the start of the current change log” here is a possible cause:
The time between deployments is too long. This means that the information regarding the last deployment has been already deleted from the Change Log and therefore the incremental deployment process cannot find a previous entry to compare. The Change Log history is set by default to 15 days, after that all history is deleted, so you can set to a bigger timeframe or to never.
Well this is the part you might find not so good having found a possible solution . . . The proper solution is to perform a full deploy to a new content database. Another possible solution is to perform a full deploy for the same content database, but this is not advised by Microsoft because the contents that were deleted or moved since the last deployment might not be updated.
It is very important BEFORE you set the deployments to check on the Change Log settings to prevent this problem from happening. You can do in the general settings of the Web Application in the Central Administration, so:
Central Administration –> Application Management –> Web Applications General Settings
in the Change Log section you can change the settings.
You can check more information on this deployment error in the Stefan Gossner blog: http://blogs.technet.com/stefan_gossner/archive/2008/03/13/moss-common-issue-incremental-deployment-fails-with-the-changetoken-refers-to-a-time-before-the-start-of-the-current-change-log.aspx