The popularity of the single-process model has made it necessary to examine how connector deregistration and reregistration affect ManifoldCF. In particular, when you start up ManifoldCF in single-process mode, deregistration of all connectors takes place, followed by reregistration of the ones that are now in the connectors.xml file. Unfortunately, deregistration cleans up any database tables that belong to the connector.
It would be better to deregister intelligently - that is, only deregister those connectors that were deleted or whose naming/data had changed.
The place in the code where this happens is in framework/pull-agent/src/main/java/org/apache/manifoldcf/crawler/system/ManifoldCF.java. The method is reregisterAllConnectors().