When reading FCL from ArcGIS sde database, also the information about the FDS in which the FCL resides is available in FME. There is no problem in writing it to another database in a FDS, even if this FDS does not exist in the target. If one would like to create the new FCL not in a FDS (in my case SQL server database) straight from the input, you will get an error creating a FDS.

Geodatabase Writer: Creating feature class `ARCFMUT.FCL_BW_LOGGER' in feature dataset 'BW_intern.ARCFMUT.FDS_BW_DIVERSEN'

An error occurred while attempting to create the feature class 'ARCFMUT.FCL_BW_LOGGER'. The error number from ArcObjects is: '-2147220969'. The error message from ArcObjects is: {Must be the owner to perform this operation.}

After some time of investigating this issue, I concluded that the writer tries to create a FDS using the credentials of the reader, which of course did not exist in the writer, even if I explicit had left the field for a FDS to blank.

My solution was to expose the parameter 'geodb_feature_dataset' and set the value to null, then everything works. Maybe this is helpful for other FME users...