Which version of eM Client were you using?
I had the opposite experience where eM Client did a fantastic job of removing a large number of duplicates that I’d lived with for years because of an issue with a different E-mail client and a lack of a solution. It managed to get rid of ~250,000 E-Mails and my different folders became the sizes I would have expected, threads were cleaned up, and I was not aware of the loss of anything that shouldn’t be removed.
I use Exchange and wondered if there was a possibility that differences between E-mail services/providers might come into play here, but @Kim_Fisher’s response suggests to me that might not be an issue.