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We know John will leave and that Mary will like his decision.

Does the sentence sound OK?

It looks confusing to me. If it's correct, how can it be rephrased?
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It's odd because only the second 'that' is included. It is clearer like this:

We know John will leave and Mary will like his decision.

We know that John will leave and that Mary will like his decision.
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We know for certain John will leave.

Isn't this odd either?
No, not at all to me. 'That' is optionally omitted. What do you see unusual?
Is 'for sure' almost the same as 'for certain'?

Don't you use 'for sure' more often than 'for certain?

The reason I saw 'We know for certain John will leave' is unusual is I just thought if 'for certain' is placed at the beginning or the end of the sentence sounds better.
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Is 'for sure' almost the same as 'for certain'?-- Yes.

Don't you use 'for sure' more often than 'for certain?-- Not I. 'Sure' is certainly less formal than 'certain', but the choice has much to do with idiolect, I think.

The reason I saw 'We know for certain John will leave' is unusual is I just thought if 'for certain' is placed at the beginning or the end of the sentence sounds better.-- No, not at all. The position after 'know' is as natural as it is for 'for sure'. At either end is not natural at all to my ear.