I ended up using a Dictionary object to save the original folder list and then check if the looped folder existed on that list before proceeding.
Set FSO = CreateObject("Scripting.FileSystemObject")
Set startingSubFoldColl = CreateObject("Scripting.Dicitonary")
Set Folder = FSO.GetFolder(*targetFolderPath*)
For Each Subfolder in Folder.Subfolders
startingSubFoldColl.add Cstr(Subfolder),Cstr(Subfolder)
Next
For Each SubFolder in Folder.Subfolders
If startingSubFoldColl.Exists(Cstr(Subfolder)) Then
'Do Stuff
End If
Next
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