Use rsync, then move files out of folders and delete empty folders:
# starting in /tpa_pgs/
mkdir fl_se
rsync -avzh --recursive --files-from=./files_to_move/files_to_move_sefl.txt ./pgc_batches/imagery/ ./fl_se/.
# cd to region and cleanup if needed:
find ./ -mindepth 2 -type f -exec mv {} . \;
find ./ -type d -empty -delete