When scanning with any Anti-Virus, what folders should I exclude to make sure that eMClient is happy and nothing gets corrupted?
I don’t think you need to make any exclusions for anti-virus scan.
So, if Antivirus detects a virus in an email file that eMClient has downloaded and removes it, eMClient is okay with that?
If you want to be safe, I recommend excluding the storage folder in which your database is located.
The location of your database is usually by default at C:\Users[username]\AppData\Roaming\eM Client\ or you can check the it in Tools > settings > General > Storage section if you made any changes previously.