No start, no crank after battery removed for many hours

Hello,

Symptom:
No start, no crank (total silence), with the following dash lights illuminated (power steering light on, engine light on, brake light on, engine oil pressure warning light on). Scanner did not show any fault codes.

Question:
If the battery is removed from the car for 5+ hours and reinstall the battery back, will it cause the anti-thief (immobilizer system) not to recognize the chip in the key which might cause the no start, no crank issue? If so, how do you resolve this problem? Is there a way to reset it or only a Mazda dealer can do it, how much does it cost?

General information:
Let me starts by saying the car starts-up normal, no issue at all before the battery was removed. To cut the story short, this is what I did that cause the no start, no crank. I wanted to re-mount the TCM (transmission control module) to a different location due to the TCM overheating from lack of air circulation which caused the "at" fault code for many mazda owners. I wanted to be pro-active before that happens to me, I took the advice from many Mazda owners to re-mount the TCM on the firewall to avoid the overheating issue.

Before I can access, disconnect, re-mount and re-connect the TCM, I had to remove the battery entirely and disconnect the ECU or PCM mounted next to the battery box. It should be a 1 hour job but after I removed the battery and all the parts mentioned above, I was called way to work on other things. Five hours later, I came back and re-mounted the TCM to the firewall, reconnected the TCM, ECU/PCM and re-install the battery. Went in the car, turn the key and nothing happen. No start, no crank (total silence) except for the illuminated lights mentioned above.

I am thinking, maybe the battery was removed for too long (5+ hours) which caused the anti-thief system (immobilizer) not to recognize the chip inside the key anymore. However, my remote works, I can lock, unlock, armed and disarm the car. At this point, I am lost. What cause this problem and how can I resolve it? Does anyone knows how to reset or re-sync the anti-thief system to the key? Is there something I have overlook? Thank you!