Kitty,
Yes once the protocol is issued and all documents have been submitted, you are able to stay until the CRNM is issued. Now keep checking as to the process. Once in awhile it has been sent to Brasilia and Brasilia may need something additional. Our PF office was very nice and knew me and did a check online and would say, it is ok or have in the system what is required. (yes I had to wait in line each time).There was an online site (PF will give it to you or printed on protocol to check the process, but many times not updated, so best to check)
You can travel on a protocol, some have had issues returning into BR with just a protocol at the check-in on international flights unless visa (number of days) remains valid.
Check-in does not know all countries immigration systems.