Just to add Ken
If this piece of code is slightly amended to point to p instead of p2 (3rd line from bottom), then the output is nearly reached as there is no merging of the already merged files. Screen shot attached.
Problem with it though is that Folder 1PDF_1.pdf and Folder 1PDF_1.pdf should inside the MergedFiles folder and PDF_1.pdf and PDF_2.pdf should be in the Folder 1 and Folder 2 folders respectively.
'Merge pdfs in Subfolders, save merged file in subfolders,
'and copy merged pdf to p2 folder.
For i = 0 To UBound(f)
a = aFFs(f(i) & "\*.pdf")
If IsArray(a) Then
j = j + 1
pdf = f(i) & "PDF_" & j & ".pdf"
If MergePDF(a, pdf) Then FileCopy pdf, p & "PDF_" & j & ".pdf"
End If
Next i