I had an issue on 4.05 where if you have five years of Detail Ledger (2007-2012) but Fiscal Year Maintenance has prior years (1995-2006), the Recalculate Account Balances would wipe out the first (2007) Beginning Balances. As a result, I always delete those prior years from GL_FiscalYear and GL_FiscalYearDetail files. I head that was fixed and no longer necessary, but I have not tested.
Also if posting were made to a future year (like 2812), the Recalculate Account Balances calculates through that last year (creating missing Period Records) and the rebuild can take a loooong time. So I try to get rid of those future postings before I recalculate.