I believe the fix to this is. In email go to options then Email Reconciliation then under Delete On make sure its set to Mailbox and Handheld. I believe that is the correct setting.
I don't think the current version of BIS supports two-way sync on hotmail. There have been reports that it works on yahoo mail, and some other providers. I found this information using a quick SEARCH.
Maybe someone else who is more familiar with BIS email sync can chime in.
His suggestion would work exactly opposite of your problem. It would delete from your hotmail mailbox when you deleted on your handheld.
That is sort of the issue I am having with GMAIL. I finnally over the weekend got it to work so if I delete e-mail on my BB it deletes it from the gmail account.
Now if only I could figure out how to make it delete e-mails from the BB when I delete on the gmail website. Reconcile will not even make it work.
My Hotmail reconciliation used to work perfectly -- messages deleted from my computer also deleted from the phone. Then 2 weeks ago I accidentally deleted my hotmail account from BIS and had to reenter it. I noticed when I reentered that there was no box at the bottom to check for the 2 way reconciliation like there is on my other e-mail account. Now I can delete from my phone and have it reflected on my computer, but not the other way around. Support told me it doesn't work that way, but it did work that way before! The only thing I can think of is my account is old so it might have been set up while that option was still available, but when I re-entered it, it was reset to current options.