Hi,
I'm not sure which dialog you're referring to, but most Evolution settings are stored in GConf, so I'd suggest you run as the user gconf-editor, then browse to apps/evolution, and then either in calendar/prompts or mail/prompts, you'll see a number of checkboxes which drive whether Evolution prompts the user for confirmation when certain events occur, hopefully you'll find there the one corresponding to the dialog you disabled.
Regards,
Cyrille
Hmm, in evolution 2.10, I think this is controlled by the /apps/evolution/mail/prompts/expunge gconf key. I guess you could try creating that if it doesn't exist-- it may just have got deleted somehow (but I realise you're using an older version of Evolution and so it may never have existed at all.)
Another place to look would be your ~/evolution or ~/.evolution folder, there's a lot of config saved in there too, especially with older versions of evolution.