don't you have 2 FSSO CAs? It's possible connection between Fortigate and FSSO CA was interrupted (for whichever reason) and Fortigate switched to the next configured FSSO CA.
Also, there is agreement between Fortigate and FSSO CA which users would be sent to Fortigate. This agreement is based on users' group membership. It's a list of interesting member groups for Fortigate and is called "group filter". If there is change in it, it will be reflected in Fortigate.
Group filter could be configured on Fortigate itself (if you have ldap configured in FSSO Agent entry in FGT) or directly in FSSO CA (ldap is not in FGT FSSO agent config + there is Apply&Refresh button).
Could you please go to CLI and copy here output of commands:
show config user fsso
show user adgrp
show user group | grep -f fsso