If the revamp is done properly, it should have long-term benefits for SEO. You might experience a brief dip immediately, as search engines find their way round the new structure, but the gains you can make over a longer period will quickly outweigh that dip.
When I say "done properly" - they key here is that whatever URL from the old structure a visitor requests, they get the "best fit" page in the new structure. To do this, you need to set a 301 redirect on any and all pages that are moving, to take visitors to the most appropriate page. This means that (a) search engines can easily see where your content has moved to, and can transfer your rankings and listings from the old URL to the new one, and (b) anyone following an out of date link or bookmark will still get to the content they're looking for.