When running fdupes on certain folder with -d parameter

-d --delete prompt user for files to preserve and delete all
others; important: under particular circumstances,
data may be lost when using this option together
with -s or --symlinks, or when specifying a
particular directory more than once; refer to the
fdupes documentation for additional information
and selecting some duplicates, fdupes fails to conveniently suggest which command to run to execute deletion of the selected items.

After spending time on help page ("h" key + enter) one can find:

Once tagged for deletion, files can be deleted by pressing DELETE or using the 'prune' command.
So that is it the command to use.