Thank You for posting. Due to a problem in the latest release of Java (Java 6 update 22). If you have updated to this release and are running PB 22.214.171.124 or below or 126.96.36.199 or below, you will run into the problem you have described. Please update to the latest release of PB 5.5 (version 188.8.131.52) - download link: http://www.thebrain.com/products/personalbrain/download-old/ to resolve this issue. Please note that any notes that were accessed / modified while having 184.108.40.206 installed in conjunction with Java 6 update 22 will not be present after updating. If you have a backup copy of your Brain it is recommended that you replace the lost notes from your backup.
In order to further guard against this type of data loss in the future, we are working on a feature which will store prior versions of notes and other data so that even if you were to intentionally delete something you would be able to go back to a prior version.