Hi @arne,
Redo taxonomy option
One option is to redo the taxonomy assignment using these prototype SILVA 138 classifiers:
Note, you may have to retain the classifiers yourself, with the raw files provided.
There will be more news on silva taxonomy soon. So, keep your 
peeled!
Find / replace option
Otherwise you can make use of any text editor that can make use of regular expressions, in order to find D_[0-9][0-9]*__ and replace with '' / nothing, or whatever.
Alternatively, if you do not mind the unix / linux command line, you can use sed as follows:
sed 's/D_[0-9][0-9]*__//g' < input_taxonomy.txt > output_fixed_taxonomy.txt
I am sure others will double-check my sed command. But that should work.
-Best wishes!
-Mike