Was the architect bluffing?
The Architect says that if Neo exits the door to save Trinity the Matrix will crash, but nothing happens.
shareMust have been many years since I saw TMR but I don't think the architect was bluffing. (He couldn't lie as I recall).
Neo (any of the ones) carried a piece of code what will reset the matrix thus deleting the errors that accumulated over the years in its code. Neo didn't return to the source (the other door) so, the Matrix could crash in the immediate future, killing the humans who are plugged into its system.
What followed his decision to go for the door that leads to Trinity and the 3rd movie are taking place before that time of the imminent crash actually happen, not to mention that Smith changed its code completely as the virus he is.