got it working by myself. Somehow, there was a .1 inserted in the sourceProduct tag when creating the xml-file. I removed it in the xml, saved and imported the graph again. Now it works. Maybe a bug?
The error message occured when I deleted a connection in the old graph (remove source) to insert the additional module TerrainFlattening. Could be that there went something wrong internally.
These are the xml files:
working
<node id="Terrain-Correction"> <operator>Terrain-Correction</operator> <sources> <sourceProduct refid="Apply-Orbit-File"/> </sources> <parameters class="com.bc.ceres.binding.dom.XppDomElement"> ... </parameters> </node>
not working
<node id="Terrain-Correction"> <operator>Terrain-Correction</operator> <sources> <sourceProduct.1 refid="Terrain-Flattening"/> <-here 
</sources> <parameters class="com.bc.ceres.binding.dom.XppDomElement"> ... </parameters> </node>