Blev:
No expert here but I can tell you what I know.
The PCM holds all of the programming info to operate the engine. Most chips (except the SCT ones) cannot access all of the parameters. If "athensoutkast" has some problem that can only be resolved by reflashing the PCM, then he can have it done and re-install the chip. Or, he can have the PCM reflashed with the fix along with the tuning information held in the chip and then toss the chip away.