Many issues can come up when utilizing the Lotus Notes management Agent for FIM 2010 and FIM 2010 R2.
When calling into Microsoft with a support ticket regarding an import or an export on the notes MA, it will be very helpful to have turned on Lotus Notes logging and generate a NotesMA log prior to opening your case with Microsoft.
To enable logging for Lotus Notes do the following:
The log file will be written to %FIMInstallation%\Synchronization Service\Extensions\LotusDominoConnector.log
As a side note, if the LotusDominoConnector.log is 10 MB. If a log grows larger than 10 MB a new one will be created and the existing file will be renamed to LotusDominoConnector.Index.Log
Lotus Domino Connector for FIM 2010 Technical Reference