You're close, you just need to delete the file before trying to over-write it.
dim infolder: set infolder = fso.GetFolder(IN_PATH)
dim file: for each file in infolder.Files
dim name: name = file.name
dim parts: parts = split(name, ".")
if UBound(parts) = 2 then
' file name like a.c.pdf
dim newname: newname = parts(0) & "." & parts(2)
dim newpath: newpath = fso.BuildPath(OUT_PATH, newname)
' warning:
' if we have source files C:\IN_PATH\ABC.01.PDF, C:\IN_PATH\ABC.02.PDF, ...
' only one of them will be saved as D:\OUT_PATH\ABC.PDF
if fso.FileExists(newpath) then
fso.DeleteFile newpath
end if
file.Move newpath
end if
next