Sounds like you have a different setup from mine but I thought I'd share my problem and haphazard fix since it's kinda of a similar configuration.
Within a week or so after upgrading to Lion I could not longer backup to an external HD that I have had connected to Time Capsule. My set up is the following: Uverse wireless router/modem (used for wireless) --> ethernet cable --> Time Capsule (wireless turned off) --> USB hub plugged into TC --> 2 HD's connected to hub for TC backups (one for me and my wife). Aiport Express connected wirelessly and only used to stream musch to connected speakers. TC is used only as a shared drive.
Anyway, I noticed that backups weren't happening and that I could no longer see our TC, Airport Express or the attached drives. I could reconnect the all three but Time Machine wouldn't allow me to backup to them for some reason. And when I rebooted the connection wouldn't re-establish automatically. Also, the Airport Utility wouldn't even recognize that the TC was there or the Airport Express module we have in the living room. So, I connected to the TC via ethernet to see about changing the setup...but this is when the problem randomly fixed itself. Unfortunately, I don't know which step worked so I'll give you a list of what I did...it's possibly a little confusing so I apologize ahead of time:
Preface: I powered cycled both TC and my Uverse router before starting these
1) Connected to TC via ethernet
2) Entered Airport Utility and only the TC appeared (no Airport Express)
3) Turned on the wireless to the TC and reconnected the ethernet cord back to Uverse to get the internet signal (still no sign of Airport Express)
4) Changed back to the Uverse network that everything was setup on so that I could reconfigure the router/modem....
5) With the Airport Utility still open all of a sudden TC and Airport Express reappeared...and so did the USB hub drives
6) Switched back to the TC network and used Airport Utility to turn off wireless again
7) Switched back to Uverse network...TC, drives and Airport Express still visible...
8) Restarted my MBP and initiated a Time Machine backup....everything was good to go
Given this mess that I did...I'm thinking that reconnecting via ethernet and f'in with the wireless settings might have helped...but this is a total guess.
Good luck everyone...hope you can get it back the way that it was. I know I prefer my setup this way.