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The opportunity will be visible in Marketo for reporting purpose if and only if one of the contacts linked to the opportunity is sync'ed in Marketo. So for the opportunity to show in Marketo:
- You need the opportunity to have at least 1 contact attached to it with a contact role
- You need this contact to be sync'ed with Marketo
Whether the contact was first created in Marketo or Dynamics normally should not matter.
Check that you do not have a sync filter implemented and if so that the contact that you need to sync have this checkbox ticked.