This can be done by using SharePoint administration Shell.
You need to retrieve the list and loop through folders.
If the folder content type is used, you replace the content type.
# Get your site collection first
$site = Get-SPSite -Identity http://mysitecol
#if your list is in the top web:
$web = $site.RootWeb
# or if your list is in a subsite: $web = $site.OpenWeb("/mysubweb")
#then you can get your list:
$list = $web.Lists["my list display name"]
$folderCTName = "Folder"
# your content type id looks like 0x0120......
$myCTId = "<EnteryourContentTypeIDHere>"
#finally you loop through each folder, and if the content type is default folder CT, you replace it by your own content type
for($count = $list.Folders.Count; $count -ge 0; $count--)
$curItem = $list.Folders[$count]
if ($curItem.ContentType.Name -eq $folderCTName)
$curItem["ContentTypeId"] = $myCTId
it worked on my environment