$ cd thefolder # which contains the subfolders and where the PDFs should land
$ find . -name *.pdf | xargs -I {} cp -iv {} .
# find all files
# which end in .pdf
# recursively from
# the current folder
# |
# for each emitted line
# copy the output (captured by {}) to
# the specified path ('.' is the current directory)
# copy should be verbose and should ask,
# in case a file would be overwritten
Это должно скопировать ваши файлы в /thefolder/
. Если вы хотите переместить их, замените cp
на mv
.