I ran into previously mentioned checking issue (yes, even in 1.1.2) (gentoo linux, 2.6.27r7 kernel; your ebuild, all compiler optimization disabled)
I tried the suggested steps:
1- un-automanage the torrent (went ok)
2- pause the torrent (did this with a select all; POOF program died ; restarted deluge segfaulted as soon as it reached the word "sS'paused'" in ~/.config/deluge/state/torrents.state )
That one sorta "bit". Even removing that offender caused all torrents to look 'reset' as new.
One gotcha in the scheme is that I change storage into another directory (same raid5 array) according to what it might be, but still let deluge seed when needed. Lost all that info too.
Perhaps if a periodic backup of torrents.state were kept, (and/or any other files that keep track of the larger picture!) it may be a simple way to keep folks from tearing out hair

So, thanks for the good work.
cheers:-)