Time Machine server with rotated disks
In all likelihood, yes. I haven't tested this exactly, but if Time Machine detects missing files, it may run into some problems, or have to re-backup a significant portion. Part of Time Machine's versioning relies on hard linking lots of files, so when previous versions it expects to see around aren't there, bad things could happen. It's a bit of an opaque system, so it's hard to say for sure, but it's best not to muck around with your backups.

If you want some redundancy (which is certainly a good idea for your backup system), I'd suggest one of two options. The first one is to simply set up two netatalk shares as Time Machine destinations. OS X can handle multiple Time Machine disks just fine, so you may as well take advantage of that feature. Just periodically rotate which share is online.

The second option is to clone the backup disk on the server end. You'd probably want to do some sort of check to make sure it's not being actively written to, but you should be able to do a simple rsync of the data (making sure that the proper options are there to preserve resource forks, etc.) and have a second copy of your backup.