What's the best way to Fix Drawings witn Non coplaner Objects?

We get drawings from a client & alot of the entities are in either a positive or negative direction from a zero z coordinate. Some are lines which have end points that are on the wrong z plane & some have the whole object on the wrong z plane. I know there is the flatten command but what's the best way to deal with this? We do not draw in 3d & we get alot of drawings where we try to fillet two lines & we get a message that the two lines are not coplaner

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