Once every month or so -- more often if I run into a problem with my BE database (thankfully, rarer these days than, say, in versions of a year ago), I "Rebuild (Keep User Settings)", so as to do a bit of database housecleaning.
One (small) frustration of this process is that "Rebuild" doesn't preserve the window layout of the older database. In particular, the window height and "View formatted" field, which I have set to show formatted entries in List view in a size suited to my iBook desktop -- are lost. Ideally, these aspects of the database should be preserved under the scenario of "preserving" user settings.
TH