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That is pretty much standard fare when it comes to aftermarket alarms. If the car was armed with the remote, it must be disarmed with the remote.
Without knowing what alarm manufacturer made that aftermarket alarm and how it is was wired to the car (ie., if they had a key disable - allow you to disarm without the remote) - only thing you can do is always lock/unlock it the key or arm/disarm with the remote.
Also don't toss the remote - unless you plan on completely removing the "brains" and the associated wiring. If the battery dies in the car, you generally cannot reset the "brain" without the remote.
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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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