It appears that the firefox setting to clear "saved passwords" (introduced in 25/1/2011 release), does more than might be expected.
It deletes key3.db, which is generated by firefox to encrypt session data (including stored passwords and certificates). This also affects addons such as session manager. This means ticking to clear "saved passwords" will result in being unable to decrypt saved sessions, losing all session information (including open windows / tabs etc.). This is not obvious when you tick "saved passwords".
It also results in the loss of other personal certificates, which may be used to access some web sites.
This needs to be documented. If you really want to delete certificates, even when password protected by the user, perhaps it might best be done by splitting it out into a more obvious separate option.