I want to "suspend" the main loop and complete dealing with the received message which involves receiving more characters, validating the message and sending back an ACK or NAK message, before I resume the main loop. That's what I was trying to do by staying in the interrupt handler until all of the above is complete.
I still don't see what's wrong with this, and I can't see what "debris" can be left

what if, because of noise or whatever, you do not get a complete message. Do you want yor thingy to just sit there??? how will you ever get the NAK sent back??

Erik