Ran into a similar issue while changing around stuff using the command line (ok, so I can't help it, I'm terrible that way ). I was stumped at first myself, read up a bit on tracker and ended up using one of the prescribed methods there, which, if memory serves me right, was running tracker-processes -r as user in an xterm.

Before you do, please re-check on that, as my memory is flaky already

And be prepared re-indexing will take a while.

Regards,
Chris.