Modern Vespa

Customer brought in Piaggio MP3 400IE for repair after sitting in their garage for 3 years after it died on their last ride. Not being a dealer, I was able, over time, to figure out all issues related to it dying in the first place, which started with a pickup (speed sensor) going bad, a bad fuel pump, a bad injector, and a brittle plastic water pump housing.
Additional issues included dirty wire connections at the relays for fuel pump and starter circuit. Dirty connectors at the starter switch and tilt/lock switch. The tilt lock system was bled to eliminate the insistent 1 second beep and appears all is functional although the seat sensor does not restrict the RPMs to under 2000 RPM if on the stand and no one on the seat. Still a win tho as all the warning lights on dash are off and unit functions properly.
Having had most of the front plastic off, side and rear plastic off and fuel tank cover plastic off. when doing testing through out diagnoses of the before mentioned issues, the saddle remote solenoid would function, was programable, and actuated properly.
Now after replacing all plastic, checking all functions and switches to be sure they work, suddenly the remote for key no longer opens the seat or saddle even after reprograming. The batteries test 3 volts and green light flashes. programmed to lock cylinder according to book, tested for voltage from #3 fuse to remote actuator module connector pin #4 and pin #1 from key fuse #7 and both are good. Black key starts unit and remote was programmed according to book. No additional test procedures are given in service manual and blue/black wire was shorted to black connector for 10 sec to forget remote code then attempt to reprogramed was performed.
Is it possible remote module failed or key lock immobilizer is ignoring relearn sequence? Open to ideas.

To clarify, the main issue to resolve is the remote control for the storage compartment? Does the bike otherwise run fine and in safe street / highway riding condition with all other functions working normally?

Reading through the description its reported that everything was working right up until the plastics where replaced. My fist thought would be that installing the plastics loosened a connection for the circuit or the cabling required to unlatch the storage compartment. Other than that I've no specific suggestions.

Or the cable to the lock is pinched somewhere

Bike is fully functional with the exception of an occasional code U1600 which is a CAN code supposedly related to the RF collar at the top of the ignition lock assembly which reads the RF chip for the key. Turning the key off, then back on generally resolves this issue. Customer does not want to replace collar unless it completely fails. It also gets an Excess Voltage code for some reason when the voltage approaches 14V to 14.2V. The schematics shows 2 wires from the Remote Control module pin #11 & pin #12 going to the antitheft reset. I tested the output wires going to both the saddle bag release motor and the seat motor independent of the Remote module and both motors release the seat and saddle bag latches properly as separate circuits.
It is my belief that either the ignition lock is not seeing the frequency of the transmitter for the remote in the initial programing procedure, the Remote Control module is not receiving that signal or the antitheft unit is ignoring it. a continuity test of the wires form pin #11 & 12 to the reset module shows both wires are good.
After talking to the customer, he had similar issues before and decided he was ok with opening the saddle bag manually with the ignition key and reaching through to open the seat manually.
I still want to find the reason it quit working so that on his next service I can try to correct the issue as I hate sending a unit out the door back to a customer with known issue even if I have to wave the labor to finish the job. They pay the bill tho so, they make the ultimate decision on what happens.