Proper protocol when changing permalinks of a website is to 301 redirect the old pages to the new pages.
At this point your old permalinks redirect to the main page and I am assuming it is simply 404ing as you have 404 to set up to redirect to home (which isn't really recommended either IMO). edit: looks like https://bitcoinarmory.com/download/troubleshooting/ is 301 redirecting to itself. It may be possible that a 301 was attempted but an error was made)
This is very bad for SEO. You are losing all of the past "juice" your former pages had when you changed the URL structure (permalinks) without applying a 301 redirect.
Curious if you have lost search traffic from the time before you made the change to the website. I would definitely recommend 301 redirecting all the changed pages (it must be a 301, any redirect will not do).
Just posting as I think this could potentially help gain/regain traffic for you. It will also help people who click the old links found by searching (as I just did) to actually go to the page they intended to land on.