I guess you have to restart the tracker. Rebooting might do the trick, but from the terminal you can control the tracker using tracker-control.

$ tracker-control -t
$ tracker-control -s

This would terminate and restart. I just accidentally the hole database by typing -r instead of -t, and it is reindexing now, so I guess that would be safe too

[edit]

Hmm, indexing complete, but now e-mails and contacts aren't indexed, or at least don't shop up in search. Also.. Something thought it was funny to wipe all contacts, which I found out after syncevolution synced the deletions to the online storage... Fortunately I had a recent back-up which could be synced back. However, contacts and e-mail are still missing in search.

[edit2]

Contacts are back in search. I guess simply reopening the contacts app was sufficient trigger for indexing. Triggering mail however is a bit more complex so it seems; new incoming mail is indexed nicely, but older mail isn't. Perhaps simply removing the account and readding it will do, being IMAP that won't be a problem.

So, to sum it up: don't use the -r parameter, unless someone knows the trick to do a proper, full reindexing including mail and contacts.