Try deleting out all the deleted e-mails in your Hotmail account (on the web browser) and all the deleted e-mails in your Hotmail account on your phone, then unsync your accounts and resync them. This may work.
On a related note, when you purge your deleted e-mails folder in your Hotmail account on your browser, take notice of how old your oldest deleted e-mails are. If your situation is anything like mine (I've had similar issues and the solution above does provide a short-term solution for a few weeks), your deleted e-mails folder will include e-mails back to the time you linked your Windows Phone to your Hotmail account. When Hotmail is not linked to a Windows Phone, deleted e-mails before a certain date are purged automatically.
One final thing - I recently went through my Hotmail account and deleted out a whole bunch of e-mails in my inbox, reducing the number of e-mails from 1100-1200 to 220. I also changed the length of time to sync the Inbox from 2 weeks to no time limit (i.e. all e-mails in my Hotmail inbox on the browser also show up on the phone). I only did that this past weekend, but so far, so good in terms of Hotmail syncing between the browser and the Windows Phone.
BTW, which Windows Phone do you own? The last few days I've considered creating a post asking people what kind of Hotmail problems they have had, if any, what device they have, what settings they have on their Hotmail account on the phone, how old their Hotmail account is, and how many e-mails they have in their inbox. Other people have had similar Hotmail syncing problems, and I want to try to figure out what the problem might be.