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You can flush it out just like normal, won't hurt the ABS system. There isn't a diagnostic mode to open the relays internal to the ABS unit. What I've done on my previous 2003 Matrix XRS is flush the brakes with fresh fluid, then while testing them out - slam the brakes on hard enough to kick on the ABS. Then repeat the flush, if desired.
As for capacity - depends on how you flush the system and if there was any air in there to begin with. I've never used more than two little bottles (8 - 12 oz each) for maintenance related flushing (every 2 years or 30K miles) and that was even being pretty generous with the flush.
If you have a power bleeder system, might need to pick up a 32 oz bottle, as you don't want accidentally want to pick up any air. Generally, you don't want to end up with too much extra fluid around, as it doesn't store well. Even when tightly capped, it will slowly absorb moisture given enough time. Best to due flushes with fresh fluid everytime, as the interval is so long between flushes.
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2002 Corolla S, 1.8L 1ZZ-FE VVT-i
2003 Matrix XRS, 1.8L 2ZZ-GE, VVTL-i (RIP)
2009 Matrix XRS, 2.4L 2AZ-FE VVT-i
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