Are both correct: If they find out you did then they probably won't reinstate you.
VS
If they found out you did then they probably won't reinstate you.
Either is correct; however, both sentences require prior context. "). Also, I'd strongly recommend that you use a comma before "then".
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Either is correct; however, both sentences require prior context. Otherwise, they look incomplete ("if they find out you did - without prior context, I'd ask, "did what?").
Also, I'd strongly recommend that you use a comma before "then". E.g., If they find out you did, then they probably won't reinstate you.