Yep. You'll probably find that the points didn't merge for one of two reasons:
(1) You mirrored over the X=0 (or Y=0 or Z=0) axis, but your centerline points weren't actually exactly on the axis
(2) You didn't mirror exactly on the axis.
Before performing the mirror operation, select all the points along your centerline, and use the set value tool (Ctrl-V) to align them on the axis. Then, when you mirror, after dragging out your mirror plane, use the numeric panel to set the plane origin to the 0 point on the correct axis.
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