I've gone through the pardot API documentation, but have not found anything related to merging/deduplicating pardot prospects though the pardot API. We have a scenario where we are getting a lot of duplicates in our pardot instance. And also we have defined a criteria of considering which of these prospects are duplicates. Since this number is huge, we wouldn't want to spend hours manually merging all of these duplicate prospects. Would be glad if Pardot rolls out an additional method within its APIs.
Please vote up this idea if you're facing the same issue.