Disconnect all users from FileMaker Server.
Save this shell script in /Library/FileMaker Server/Data/Scripts.
Execute as system script in any schedule when you need to free up the service for any task...
#!/bin/sh
# to be kind, send a message to warn connected users...
#/Library/FileMaker\ Server/Database\ Server/bin/fmsadmin -u admin -p verysecret send -m "will disconnect FileMaker services right now" -w0 -t5 -y
# then just kickoff everyone
/Library/FileMaker\ Server/Database\ Server/bin/fmsadmin -u admin -p verysecret disconnect client -m 'maintenance pause, sorry' -w0 -t5 -y