In theory it shouldn't. You should make a backup copy of your %APPDATA/deluge folder just in case. Why not upgrade all the way to 1.3.12? thanks and thanks to guy above ooh i didn't see that my private tracker allows 1.3.11, but not 1.3.12 ill upgrade to that instead of 1.3.6 im still waiting for a...

i did what you want with labelplus, detecting 720p for shows and 1080p for anime
but thats extremely broad and you're doing extremely specific (folder per show) so i dont think you'll want to use my method

Will it clear my torrent list?
I have multiple trackers seeding using LabelPlus & SeedTime plugins.
It'll be quite tedious to re-add and re-setup all of that and I'm only upgrading from 1.3.5 to 1.3.6 for a single bugfix, so it might not even be worth it.
Thanks in advance.