Bluetooth: Controller: Fix MIC failure when 2 CISes in Peripheral

Fix MIC failure when 2 or more CISes in Peripheral is active
and any CIS before the last CIS does not have reception that
lead to the event count and payload count being incorrect.
Add the missing flush implementation when switching between
CISes in the CIG event.

Signed-off-by: Vinayak Kariappa Chettimada <vich@nordicsemi.no>