Hi, and welcome to the forums.
As Barry says, your best bet is probably to erase the disk and let TM start fresh.
The first part of your problem comes from the way your backups are stored. Time Machine stores your backups in a folder named
Backups.backupdb. But when they're done over a network, that folder is placed inside a rather odd container called a +sparse bundle.+ The two are not compatible; that's why TM started a new "sequence" when you moved the HD to your Airport.
The second part may have come from the way you deleted things. If you used the Finder to delete any part of either set of backups, that set is now corrupted. From your description, it sounds like you deleted some from the sparse bundle. One of the oddities of a sparse bundle is, it doesn't automatically contract when you delete things from it; that's a separate operation.
So you have a decision to make: do you want to continue with the backups directly attached, or via your Airport? Unfortunately, using the Airport is not officially supported by Apple:
http://docs.info.apple.com/article.html?path=Mac/10.6/en/15139.html. It does work well for some folks, not so well for some, and not at all for others. If you get it to work well now, for you, there's always the possibility a future update will render it useless.
If you want to continue wirelessly, your best bet is, as Barry says, to erase the disk and start over.
If you want to continue with the disk directly-attached, then delete the entire sparse bundle via the Finder. Before continuing, however,
Repair the TM drive -- see #A5 in the
Time Machine - Troubleshooting *User Tip,* also at the top of this forum.
If the backups you deleted were in the
Backups.backupdb folder (made while directly-attached), you
may be able to continue using them, if the +*Repair Disk+* is able to repair them, but you may have lost some disk space. If so, the only way to recover it is to erase the disk and start over.