Thanks Toby, setting 'Alert Reminder Frequency" to 0 helped with not getting a notification for Probes even after SIA restart during the maintenance window.
However, watches on BO servers( like event server, CMS, ADP serer) do send the notifications after the SIA restarts during the maintenance window.( which is correct technically).
However, we don't want watches to monitor the servers during the maintenance window. So is there feature or setting that can be used so that watches skip the server monitoring during the maintenance window and we can avoid false notification/alert ?