Codes marked Permanent - Scan tool does not erase?? P0102, P0113, P0017, P219A

[Sm1nts2escape]

I recently built a new engine for a 2013 that I got that had a spun rod bearing. When I started the car with the new engine I noticed after it warmed up it dropped to a low idle, the throttle became twitchy, wanted to stall and had the check engine light and slip light on. I put a scan tool on it and I have 4 codes p0102 - Mass or Volume air flow circuit low input, p0113 - Intake air temp circuit high input, p0017 - Crankshaft position camshaft position correlation bank 1 sensor b and P219a - Bank 1 Air-fuel imbalance. All four codes are marked permanent. When I delete them they are immediately there again once the scan tool rescans... Will these codes remove themselves when the issue is found and fixed or do I have to reflash the ecu or something else? I tried disconnecting the battery and joining the power wires together to drain the capacitors in the ecu with no luck to drop the codes.

[RZNT4R]

Those codes are permanent specifically so they are not erased/battery disconnected to pass inspections.

The monitors need to pass for the ECM to clear them.