Many users I know have always complained that the BlackBerry calendar deletes all appointments older than 90 days. After reading a recent RIM Knowledgebase article I found that this is a known bug. It turns out that this is actually a symptom of using the BlackBerry Desktop redirector. The redirector installs an CICAL service book that sets all appointments to delete after 90 days. The problem is that only BES users have the option to change this to a longer date or remove the auto delete.
RIM has posted a fix for users in this situation by following these instructions to keep appointments forever on your BlackBerry. Just read the workaround at the bottom of the knowledgebase article at this link and follow the instructions to the letter to keep your appointments forever on your Berry.