Be sure to add references commented in the code and replace paths in p1, p2, and p3.

'Early Binding method for fso and d requires Reference: MicroSoft Scripting Runtime, scrrun.dll
Sub Main()
  Dim p1 As String, p2 As String, p3 As String, f As String
  Dim d As New Dictionary, e, fso As New FileSystemObject
  Dim a(), b()
  
  '*** Set folder paths to suit ***
  p1 = "C:\Users\lenovo1\Dropbox\Excel\pdf\Acrobat\Sets\Set A\" 'Cover sheet PDFs
  p2 = "C:\Users\lenovo1\Dropbox\Excel\pdf\Acrobat\Sets\Set B\" 'Matching deta PDFs
  p3 = "C:\Users\lenovo1\Dropbox\Excel\pdf\Acrobat\Sets\Set C\ 'Merged PDF folder"


  'Get full pdf filenames in folders.
  a() = aFFs(p1 & "*.pdf")  '& "*.pdf" not needed if only PDFs in p1.
  b() = aFFs(p2 & "*.pdf")
  
  'Create dictionay from b() for easy matching scheme.
  For Each e In b()
    d.Add fso.GetFileName(e), Nothing
  Next e
  
  'Iterate each file in p1, match to p1, and merge to p3 if exists in p2.
  For Each e In a()
    f = fso.GetFileName(e)
    If d.Exists(f) Then MergePDFs e & "," & p2 & f, p3 & f
  Next e
End Sub

'Command line switches for the shell's Dir, http://ss64.com/nt/dir.html
Function aFFs(myDir As String, Optional extraSwitches = "", _
  Optional tfSubFolders As Boolean = False) As Variant
  
  Dim s As String, a() As String, v As Variant
  Dim b() As Variant, i As Long
  
  If tfSubFolders Then
    s = CreateObject("Wscript.Shell").Exec("cmd /c dir " & _
      """" & myDir & """" & " /b /s " & extraSwitches).StdOut.ReadAll
    Else
    s = CreateObject("Wscript.Shell").Exec("cmd /c dir " & _
      """" & myDir & """" & " /b " & extraSwitches).StdOut.ReadAll
  End If
  
  a() = Split(s, vbCrLf)
  If UBound(a) = -1 Then
    MsgBox myDir & " not found.", vbCritical, "Macro Ending"
    Exit Function
  End If
  ReDim Preserve a(0 To UBound(a) - 1) As String 'Trim trailing vblfcr
  
  For i = 0 To UBound(a)
    If Not tfSubFolders Then
      s = Left$(myDir, InStrRev(myDir, "\"))
      'add the folder name
      a(i) = s & a(i)
    End If
  Next i
  aFFs = sA1dtovA1d(a)
End Function


Function sA1dtovA1d(strArray() As String) As Variant
  Dim varArray() As Variant, i As Long
  ReDim varArray(LBound(strArray) To UBound(strArray))
  For i = LBound(strArray) To UBound(strArray)
    varArray(i) = CVar(strArray(i))
  Next i
  sA1dtovA1d = varArray()
End Function


Sub MergePDFs(MyFiles As String, DestFile As String)
     ' Reference required: VBE - Tools - References - Acrobat
     
    Dim a As Variant, i As Long, n As Long, ni As Long
    Dim AcroApp As New Acrobat.AcroApp, PartDocs() As Acrobat.CAcroPDDoc
     
    a = Split(MyFiles, ",")
    ReDim PartDocs(0 To UBound(a))
     
    On Error GoTo exit_
    If Len(Dir(DestFile)) Then Kill DestFile
    For i = 0 To UBound(a)
         ' Check PDF file presence
        If Dir(Trim(a(i))) = "" Then
            MsgBox "File not found" & vbLf & a(i), vbExclamation, "Canceled"
            Exit For
        End If
         ' Open PDF document
        Set PartDocs(i) = CreateObject("AcroExch.PDDoc")
        PartDocs(i).Open Trim(a(i))
        If i Then
             ' Merge PDF to PartDocs(0) document
            ni = PartDocs(i).GetNumPages()
            If Not PartDocs(0).InsertPages(n - 1, PartDocs(i), 0, ni, True) Then
                MsgBox "Cannot insert pages of" & vbLf & a(i), vbExclamation, "Canceled"
            End If
             ' Calc the number of pages in the merged document
            n = n + ni
             ' Release the memory
            PartDocs(i).Close
            Set PartDocs(i) = Nothing
        Else
             ' Calc the number of pages in PartDocs(0) document
            n = PartDocs(0).GetNumPages()
        End If
    Next
     
    If i > UBound(a) Then
         ' Save the merged document to DestFile
        If Not PartDocs(0).Save(PDSaveFull, DestFile) Then
            MsgBox "Cannot save the resulting document" & vbLf & DestFile, vbExclamation, "Canceled"
        End If
    End If
     
exit_:
     
     ' Inform about error/success
    If Err Then
        MsgBox Err.Description, vbCritical, "Error #" & Err.Number
    ElseIf i > UBound(a) Then
        MsgBox "The resulting file was created in:" & vbLf & DestFile, vbInformation, "Done"
    End If
     
     ' Release the memory
    If Not PartDocs(0) Is Nothing Then PartDocs(0).Close
    Set PartDocs(0) = Nothing
     
     ' Quit Acrobat application
    AcroApp.Exit
    Set AcroApp = Nothing
End Sub