This is from Vexengo's website:
"Later, after performing the deconvolution, you may need to edit the resulting impulses to fit your needs. For example, you may need to cut the leading and/or trailing silence. Also, you may need to add fade-ins and/or fade-outs. Voxengo Deconvolver does not require the recording to be "in sync" with the test tone - you may add as much pre- and post-silence as you need."