Does anyone have any idea what would cause an ECU to only communicate while in Boot Mode?

The ecu is a 4b0906018DA, I immo deleted it and had it working fine in my 03 GTi. Aside from it being in limp all the time from overboost protection and being coded incorrectly. I tried translating my 032LP tune to the DA. After a few flashes[bench setup] I couldnt read the ecu using VCDS. Galletto just freezes, NefMotoECUFlasher Doesnt connect either way, and MPPS just states ECU No Reply. I can force Boot Mode and read and write just fine using both Gal and MPPS with no errors. But No matter what, outside of Boot Mode I have No Comms... Ive tried flashing the orig bins I ripped as backups. I pulled them with Gal and MPPS for redundancy. I set MPPS to read Full Data. I tried flashing DA Bins I sourced here and other forums. No luck.

I also could no longer read eeprom using ME7EEPROM, and writing resulted in Fail over and over. It fails during "Loader + MonitorCore Sending ... MonitorCore"

I read somewhere that when you read eeprom data, you dont read it entirely and rewriting it could corrupt it if you write over it and then replace it. Im I understanding this correctly? Could this be a cause? If so, Is there a way to extract the eeprom data from a .Bin File? I tapped into my eeprom directly and read it using my TL866ii Programmer and flashed my eeprom file to the chip. Which didnt solve anything.

Anyhow, I would appreciate any ideas. Thx