During Pootle development databases can get into unusable states, searching indexes can be corrupted, … This page lists places to look for when things are broken.
Pootle indexes each language in every project if PyLucene or Xapian are available.
The indices are stored under .translation_index under a language directory (for example pootle/eu/.translation_index). Corrupt indices might cause problems. Deleting the .translation_index directories will cause Pootle to regenerate the indices.
Also have a look at the files generated by the Translate Toolkit.
Since Pootle 2.0, you can also check the dbs/ directory (and your database if you are using one) to entirely delete things you are working on if you want to start cleanly.