We have resolved this so I thought I would share in case anyone else has a similar problem. Because we had to recreate the certificate activity in our classes after upgrading, we lost the "Link to next activity" in the previous lesson's settings so the Certificate was not showing up at the end of the lesson. We went into that setting in the last lesson before the certificate and set it to link the certificate so we can now see it. Hope that helps anyone who comes across the same issue.
Custom certificate (plugin)
link to certificate at end of lesson
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