1. Can someone guide me on how to delete the files (using a win 7 pc + putty)
2. If i add any torrents now in transmission it does not get saved to my external HDD. How to rectify this?
1. You CAN'T. Windows has no (sensible) way to access an ext4 filesystem
2. Look at /etc/fstab and how you get your HDD mounted. Using UUID in /etc/fstab is more reliable than using /dev/sda1
To fix your problem you will need a USB SDCard reader and a NEW SDCard.
1. Build a new copy of Raspbian (or NOBS/Raspbian) on the NEW SDCard and boot that in your RPi.
2. Connect your external HDD and mount the filesystem
3. Connect your new USB SDCard reader, insert the FULL SDCard in that reader and mount the filesystem
4. Move files from FULL SDCard to HDD freeing up the space
5. Sync everything and umount
6. Shutdown your Raspbian rescue system
7. Pull the NEW SDCard and re-insert the now less than FULL SDCard
9. Grab a beer and celebrate a job well done
Now that you have a second SDCard and a USB SDCard reader you can start taking weekly backups of your SDCard that way next time you screw up all you'll need to do is shutdown, pull the SDCard and reboot the system from your backup SDCard.