Clean Import plug-in

[Diana Stock]

Hello all,
I have used the Clean Import plug-in (v3.1) and wonder if anyone else
out there has used it? 
 
The plug-in is a great tool, but I don't know what I am doing wrong (at
this point, I don't mind revealing my ignorance). Does anyone know if it
removes old text flows and replaces them with new? 
 
My new template has one flow (A) compared to the old template having two
(A and Graphic, not connected). When I use the plug-in, the page with
the Graphic flow remains on the Body page -  with the new flow. To
remove the Graphic flow, I have to edit each file and manually delete
it. Is it me or memor(ex)? My memory does seems to escape me lately.
:-)
 
Any advise is greatly appreciated,

Diana Stock
Southwest Airlines
214-792-7433