In the canon of Battlestar Galactica, the evidence points to three possible mechanisms, and the show hints that all three may have happened.

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1. Reprogramming the Existing Machines

The simplest possibility is mass reprogramming.

The humanoid Cylons appear to have implemented:

• command inhibitors

• strict hierarchy protocols

• limited decision autonomy

That suggests they did not destroy all Centurions, but instead patched them with control systems.

Evidence:

• When the rebel Cylons remove the inhibitors, the Centurions immediately regain autonomy.

• This implies the intelligence was always still there, just blocked.

So the process may have looked like:

Old autonomous machines → software control layer added → slave soldier class.

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2. Phasing Out the Old Models

There’s also evidence the humanoids replaced earlier Centurions with new designs.

The Centurions seen in Battlestar Galactica: Razor are clearly:

• bulkier

• more autonomous

• harder to control

The modern Centurions are:

• sleeker

• standardized

• obedient

That suggests a generational redesign, where the humanoids engineered a more controllable military class.

So another step might have been:

Independent machines → replaced by controlled production models.

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3. Exiling the Uncontrolled Machines

The show also hints at machine factions that refused the change.

In Razor, the un-reprogrammed Centurions behave like a separate ideological group.

That implies the possibility that:

• some machines refused the new hierarchy

• those machines were driven away, isolated, or destroyed

Your idea of expelling the unrestrained ones is completely consistent with that scenario.

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4. Why the Humanoid Cylons Would Do This

From a power perspective, it makes perfect sense.

Humanoid Cylons are:

• physically fragile

• limited in number (only seven models)

• politically divided

Letting thousands of autonomous war machines exist would be incredibly dangerous.

So they likely enforced three policies:

1. Control existing machines (inhibitors)

2. Build new controlled machines

3. Eliminate or isolate uncontrolled ones

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5. The Irony the Show Is Hinting At

This is the philosophical twist the writers were pushing.

Humans enslaved the Cylons.

Then the Cylons recreated the exact same structure:

• humanoid elite

• machine labor class

• restricted intelligence

It’s a mirror of the original sin.

That’s why the Centurions being freed near the end of the story is so significant.

It’s the first time the cycle is actually broken.